Contact Information
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski, PhD
Battelle Center for Mathematical MedicineAbigail Wexner Research Institute700 Children’s DriveColumbus, Ohio 43205 (map)
Learn more about Andrzej Kloczkowski
Research
Lab(s)
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Publications
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120: e2214423119.
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules. 2023 Jan 3; 28:
Hassan M, Shahzadi S, Kloczkowski A. Tyrosinase Inhibitors Naturally Present in Plants and Synthetic Modifications of These Natural Products as Anti-Melanogenic Agents: A Review. Molecules. 2023 Jan 2; 28:
Hassan M, Amir A, Shahzadi S, Kloczkowski A. Therapeutic Implications of microRNAs in Depressive Disorders: A Review. Int J Mol Sci. 2022 Nov 4; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Álvarez-Machancoses Ó, Bea G, Galmarini CM, Kloczkowski A. Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput Biol Med. 2022 Oct; 149: 106029.
Hosseini Nasab N, Raza H, Shim RS, Hassan M, Kloczkowski A, Kim SJ. Potent Alkaline Phosphatase Inhibitors, Pyrazolo-Oxothiazolidines: Synthesis, Biological Evaluation, Molecular Docking, and Kinetic Studies. Int J Mol Sci. 2022 Oct 31; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Fernández-Brillet L, Cernea A, Kloczkowski A. Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space. Int J Mol Sci. 2022 Oct 26; 23:
Irfan A, Zahoor AF, Kamal S, Hassan M, Kloczkowski A. Ultrasonic-Assisted Synthesis of Benzofuran Appended Oxadiazole Molecules as Tyrosinase Inhibitors: Mechanistic Approach through Enzyme Inhibition, Molecular Docking, Chemoinformatics, ADMET and Drug-Likeness Studies. Int J Mol Sci. 2022 Sep 19; 23:
Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS Omega. 2022 Jun 14; 7: 19243-19260.
Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci. 2022 Jun 30; 23:
Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci. 2022 Apr 22; 23:
Hassan M, Vanjare BD, Sim KY, Raza H, Lee KH, Shahzadi S, Kloczkowski A. Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase. Molecules. 2022 Mar 7; 27:
Li MS, Kloczkowski A, Cieplak M, Kouza M. Final Remarks. Methods Mol Biol. 2022; 2340: 469-470.
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol. 2022; 2340: 41-50.
Hassan M, Iqbal MS, Naqvi S, Alashwal H, Moustafa AA, Kloczkowski A. Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches. Front Mol Biosci. 2022; 9: 866072.
Hassan M, Zahid S, Alashwal H, Kloczkowski A, Moustafa AA. Mechanistic insights into TNFR1/MADD death domains in Alzheimer's disease through conformational molecular dynamic analysis. Sci Rep. 2021 Jun 10; 11: 12256.
Agrawal S, Ransom RF, Saraswathi S, Garcia-Gonzalo E, Webb A, Fernandez-Martinez JL, Popovic M, Guess AJ, Kloczkowski A, Benndorf R, Sadee W, Smoyer WE, On Behalf Of The Pediatric Nephrology Research Consortium Pnrc. Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. J Clin Med. 2021 Feb 2; 10:
Fernández-Martínez JL, Fernández-Muñiz Z, Cernea A, Kloczkowski A. Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic. Comput Math Methods Med. 2021; 2021: 5556433.
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 2021 Jan 8; 49: D298-D308.
Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods Mol Biol. 2021; 2190: 307-316.
Álvarez-Machancoses Ó, Fernández-Martínez JL, Kloczkowski A. Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules. 2020 May 26; 25:
Fernández-Martínez JL, Álvarez-Machancoses Ó, de Andrés-Galiana EJ, Bea G, Kloczkowski A. Robust Sampling of Defective Pathways in Alzheimer's Disease. Implications in Drug Repositioning. Int J Mol Sci. 2020 May 19; 21:
Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci. 2020; 7: 607323.
Alterovitz WL, Faraggi E, Oldfield CJ, Meng J, Xue B, Huang F, Romero P, Kloczkowski A, Uversky VN, Dunker AK. Many-to-one binding by intrinsically disordered protein regions. Pac Symp Biocomput. 2020; 25: 159-170.
Álvarez-Machancoses Ó, De Andrés-Galiana EJ, Fernández-Martínez JL, Kloczkowski A. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. Biomolecules. 2019 Dec 31; 10:
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci. 2019 Sep 21; 20:
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel). 2019 Aug; 21:
Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model. 2019 Feb 27; 25: 79.
Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel). 2018 Dec 3; 9:
Lan PD, Kouza M, Kloczkowski A, Li MS. A topological order parameter for describing folding free energy landscapes of proteins. J Chem Phys. 2018 Nov 7; 149: 175101.
Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci. 2018 Nov 6; 19:
Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules. 2018 Aug 10; 23:
Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn. 2018 Jul; 36: 2331-2341.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Gieldon A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Slusarz M, Slusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popovic Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Oldziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Foldit Players consortium., Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018 Jul 2; 8: 9939.
Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys. 2018 Jun 7; 148: 215106.
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol. 2018 Apr; 16: 1850005.
View More Publications
Biography
Andrzej Kloczkowski is Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He is a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski’s NIH-funded research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
View My Publications Connect on LinkedIn Connect on Google Scholar
See Andrzej Kloczkowski’s Curriculum Vitae (CV)
Academic and Clinical Areas
Battelle Center for Mathematical Medicine
Faculty
Kloczkowski Lab
Principal Investigator
Primary Department
Battelle Center for Mathematical Medicine
Professional Experience
2010 - Present Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Principal Investigator,2007 - 2010 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist II2005 - 2010 Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Adjunct (Full) Professor2002 - 2007 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist I
Contact Information
Battelle Center for Mathematical Medicine
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski
Abigail Wexner Research Institute700 Children's DriveColumbus, Ohio 43205 (map)
Contact Information
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski, PhD
Battelle Center for Mathematical MedicineAbigail Wexner Research Institute700 Children’s DriveColumbus, Ohio 43205 (map)
Learn more about Andrzej Kloczkowski
Research
Lab(s)
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Publications
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120: e2214423119.
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules. 2023 Jan 3; 28:
Hassan M, Shahzadi S, Kloczkowski A. Tyrosinase Inhibitors Naturally Present in Plants and Synthetic Modifications of These Natural Products as Anti-Melanogenic Agents: A Review. Molecules. 2023 Jan 2; 28:
Hassan M, Amir A, Shahzadi S, Kloczkowski A. Therapeutic Implications of microRNAs in Depressive Disorders: A Review. Int J Mol Sci. 2022 Nov 4; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Álvarez-Machancoses Ó, Bea G, Galmarini CM, Kloczkowski A. Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput Biol Med. 2022 Oct; 149: 106029.
Hosseini Nasab N, Raza H, Shim RS, Hassan M, Kloczkowski A, Kim SJ. Potent Alkaline Phosphatase Inhibitors, Pyrazolo-Oxothiazolidines: Synthesis, Biological Evaluation, Molecular Docking, and Kinetic Studies. Int J Mol Sci. 2022 Oct 31; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Fernández-Brillet L, Cernea A, Kloczkowski A. Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space. Int J Mol Sci. 2022 Oct 26; 23:
Irfan A, Zahoor AF, Kamal S, Hassan M, Kloczkowski A. Ultrasonic-Assisted Synthesis of Benzofuran Appended Oxadiazole Molecules as Tyrosinase Inhibitors: Mechanistic Approach through Enzyme Inhibition, Molecular Docking, Chemoinformatics, ADMET and Drug-Likeness Studies. Int J Mol Sci. 2022 Sep 19; 23:
Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS Omega. 2022 Jun 14; 7: 19243-19260.
Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci. 2022 Jun 30; 23:
Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci. 2022 Apr 22; 23:
Hassan M, Vanjare BD, Sim KY, Raza H, Lee KH, Shahzadi S, Kloczkowski A. Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase. Molecules. 2022 Mar 7; 27:
Li MS, Kloczkowski A, Cieplak M, Kouza M. Final Remarks. Methods Mol Biol. 2022; 2340: 469-470.
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol. 2022; 2340: 41-50.
Hassan M, Iqbal MS, Naqvi S, Alashwal H, Moustafa AA, Kloczkowski A. Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches. Front Mol Biosci. 2022; 9: 866072.
Hassan M, Zahid S, Alashwal H, Kloczkowski A, Moustafa AA. Mechanistic insights into TNFR1/MADD death domains in Alzheimer's disease through conformational molecular dynamic analysis. Sci Rep. 2021 Jun 10; 11: 12256.
Agrawal S, Ransom RF, Saraswathi S, Garcia-Gonzalo E, Webb A, Fernandez-Martinez JL, Popovic M, Guess AJ, Kloczkowski A, Benndorf R, Sadee W, Smoyer WE, On Behalf Of The Pediatric Nephrology Research Consortium Pnrc. Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. J Clin Med. 2021 Feb 2; 10:
Fernández-Martínez JL, Fernández-Muñiz Z, Cernea A, Kloczkowski A. Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic. Comput Math Methods Med. 2021; 2021: 5556433.
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 2021 Jan 8; 49: D298-D308.
Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods Mol Biol. 2021; 2190: 307-316.
Álvarez-Machancoses Ó, Fernández-Martínez JL, Kloczkowski A. Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules. 2020 May 26; 25:
Fernández-Martínez JL, Álvarez-Machancoses Ó, de Andrés-Galiana EJ, Bea G, Kloczkowski A. Robust Sampling of Defective Pathways in Alzheimer's Disease. Implications in Drug Repositioning. Int J Mol Sci. 2020 May 19; 21:
Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci. 2020; 7: 607323.
Alterovitz WL, Faraggi E, Oldfield CJ, Meng J, Xue B, Huang F, Romero P, Kloczkowski A, Uversky VN, Dunker AK. Many-to-one binding by intrinsically disordered protein regions. Pac Symp Biocomput. 2020; 25: 159-170.
Álvarez-Machancoses Ó, De Andrés-Galiana EJ, Fernández-Martínez JL, Kloczkowski A. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. Biomolecules. 2019 Dec 31; 10:
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci. 2019 Sep 21; 20:
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel). 2019 Aug; 21:
Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model. 2019 Feb 27; 25: 79.
Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel). 2018 Dec 3; 9:
Lan PD, Kouza M, Kloczkowski A, Li MS. A topological order parameter for describing folding free energy landscapes of proteins. J Chem Phys. 2018 Nov 7; 149: 175101.
Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci. 2018 Nov 6; 19:
Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules. 2018 Aug 10; 23:
Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn. 2018 Jul; 36: 2331-2341.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Gieldon A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Slusarz M, Slusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popovic Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Oldziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Foldit Players consortium., Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018 Jul 2; 8: 9939.
Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys. 2018 Jun 7; 148: 215106.
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol. 2018 Apr; 16: 1850005.
View More Publications
Biography
Andrzej Kloczkowski is Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He is a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski’s NIH-funded research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
View My Publications Connect on LinkedIn Connect on Google Scholar
See Andrzej Kloczkowski’s Curriculum Vitae (CV)
Academic and Clinical Areas
Battelle Center for Mathematical Medicine
Faculty
Kloczkowski Lab
Principal Investigator
Primary Department
Battelle Center for Mathematical Medicine
Professional Experience
2010 - Present Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Principal Investigator,2007 - 2010 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist II2005 - 2010 Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Adjunct (Full) Professor2002 - 2007 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist I
Contact Information
Battelle Center for Mathematical Medicine
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski
Abigail Wexner Research Institute700 Children's DriveColumbus, Ohio 43205 (map)
Contact Information
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski, PhD
Battelle Center for Mathematical MedicineAbigail Wexner Research Institute700 Children’s DriveColumbus, Ohio 43205 (map)
Learn more about Andrzej Kloczkowski
Contact Information
- Call us at:
- (614)355-5622
- Fax us at:
- (614) 355-6671
- Email Andrzej Kloczkowski, PhD
- Battelle Center for Mathematical MedicineAbigail Wexner Research Institute700 Children’s DriveColumbus, Ohio 43205 (map)
Learn more about Andrzej Kloczkowski
Research
Lab(s)
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Publications
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120: e2214423119.
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules. 2023 Jan 3; 28:
Hassan M, Shahzadi S, Kloczkowski A. Tyrosinase Inhibitors Naturally Present in Plants and Synthetic Modifications of These Natural Products as Anti-Melanogenic Agents: A Review. Molecules. 2023 Jan 2; 28:
Hassan M, Amir A, Shahzadi S, Kloczkowski A. Therapeutic Implications of microRNAs in Depressive Disorders: A Review. Int J Mol Sci. 2022 Nov 4; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Álvarez-Machancoses Ó, Bea G, Galmarini CM, Kloczkowski A. Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput Biol Med. 2022 Oct; 149: 106029.
Hosseini Nasab N, Raza H, Shim RS, Hassan M, Kloczkowski A, Kim SJ. Potent Alkaline Phosphatase Inhibitors, Pyrazolo-Oxothiazolidines: Synthesis, Biological Evaluation, Molecular Docking, and Kinetic Studies. Int J Mol Sci. 2022 Oct 31; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Fernández-Brillet L, Cernea A, Kloczkowski A. Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space. Int J Mol Sci. 2022 Oct 26; 23:
Irfan A, Zahoor AF, Kamal S, Hassan M, Kloczkowski A. Ultrasonic-Assisted Synthesis of Benzofuran Appended Oxadiazole Molecules as Tyrosinase Inhibitors: Mechanistic Approach through Enzyme Inhibition, Molecular Docking, Chemoinformatics, ADMET and Drug-Likeness Studies. Int J Mol Sci. 2022 Sep 19; 23:
Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS Omega. 2022 Jun 14; 7: 19243-19260.
Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci. 2022 Jun 30; 23:
Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci. 2022 Apr 22; 23:
Hassan M, Vanjare BD, Sim KY, Raza H, Lee KH, Shahzadi S, Kloczkowski A. Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase. Molecules. 2022 Mar 7; 27:
Li MS, Kloczkowski A, Cieplak M, Kouza M. Final Remarks. Methods Mol Biol. 2022; 2340: 469-470.
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol. 2022; 2340: 41-50.
Hassan M, Iqbal MS, Naqvi S, Alashwal H, Moustafa AA, Kloczkowski A. Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches. Front Mol Biosci. 2022; 9: 866072.
Hassan M, Zahid S, Alashwal H, Kloczkowski A, Moustafa AA. Mechanistic insights into TNFR1/MADD death domains in Alzheimer's disease through conformational molecular dynamic analysis. Sci Rep. 2021 Jun 10; 11: 12256.
Agrawal S, Ransom RF, Saraswathi S, Garcia-Gonzalo E, Webb A, Fernandez-Martinez JL, Popovic M, Guess AJ, Kloczkowski A, Benndorf R, Sadee W, Smoyer WE, On Behalf Of The Pediatric Nephrology Research Consortium Pnrc. Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. J Clin Med. 2021 Feb 2; 10:
Fernández-Martínez JL, Fernández-Muñiz Z, Cernea A, Kloczkowski A. Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic. Comput Math Methods Med. 2021; 2021: 5556433.
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 2021 Jan 8; 49: D298-D308.
Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods Mol Biol. 2021; 2190: 307-316.
Álvarez-Machancoses Ó, Fernández-Martínez JL, Kloczkowski A. Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules. 2020 May 26; 25:
Fernández-Martínez JL, Álvarez-Machancoses Ó, de Andrés-Galiana EJ, Bea G, Kloczkowski A. Robust Sampling of Defective Pathways in Alzheimer's Disease. Implications in Drug Repositioning. Int J Mol Sci. 2020 May 19; 21:
Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci. 2020; 7: 607323.
Alterovitz WL, Faraggi E, Oldfield CJ, Meng J, Xue B, Huang F, Romero P, Kloczkowski A, Uversky VN, Dunker AK. Many-to-one binding by intrinsically disordered protein regions. Pac Symp Biocomput. 2020; 25: 159-170.
Álvarez-Machancoses Ó, De Andrés-Galiana EJ, Fernández-Martínez JL, Kloczkowski A. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. Biomolecules. 2019 Dec 31; 10:
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci. 2019 Sep 21; 20:
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel). 2019 Aug; 21:
Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model. 2019 Feb 27; 25: 79.
Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel). 2018 Dec 3; 9:
Lan PD, Kouza M, Kloczkowski A, Li MS. A topological order parameter for describing folding free energy landscapes of proteins. J Chem Phys. 2018 Nov 7; 149: 175101.
Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci. 2018 Nov 6; 19:
Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules. 2018 Aug 10; 23:
Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn. 2018 Jul; 36: 2331-2341.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Gieldon A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Slusarz M, Slusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popovic Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Oldziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Foldit Players consortium., Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018 Jul 2; 8: 9939.
Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys. 2018 Jun 7; 148: 215106.
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol. 2018 Apr; 16: 1850005.
View More Publications
Research
Lab(s)
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Publications
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120: e2214423119.
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules. 2023 Jan 3; 28:
Hassan M, Shahzadi S, Kloczkowski A. Tyrosinase Inhibitors Naturally Present in Plants and Synthetic Modifications of These Natural Products as Anti-Melanogenic Agents: A Review. Molecules. 2023 Jan 2; 28:
Hassan M, Amir A, Shahzadi S, Kloczkowski A. Therapeutic Implications of microRNAs in Depressive Disorders: A Review. Int J Mol Sci. 2022 Nov 4; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Álvarez-Machancoses Ó, Bea G, Galmarini CM, Kloczkowski A. Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput Biol Med. 2022 Oct; 149: 106029.
Hosseini Nasab N, Raza H, Shim RS, Hassan M, Kloczkowski A, Kim SJ. Potent Alkaline Phosphatase Inhibitors, Pyrazolo-Oxothiazolidines: Synthesis, Biological Evaluation, Molecular Docking, and Kinetic Studies. Int J Mol Sci. 2022 Oct 31; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Fernández-Brillet L, Cernea A, Kloczkowski A. Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space. Int J Mol Sci. 2022 Oct 26; 23:
Irfan A, Zahoor AF, Kamal S, Hassan M, Kloczkowski A. Ultrasonic-Assisted Synthesis of Benzofuran Appended Oxadiazole Molecules as Tyrosinase Inhibitors: Mechanistic Approach through Enzyme Inhibition, Molecular Docking, Chemoinformatics, ADMET and Drug-Likeness Studies. Int J Mol Sci. 2022 Sep 19; 23:
Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS Omega. 2022 Jun 14; 7: 19243-19260.
Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci. 2022 Jun 30; 23:
Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci. 2022 Apr 22; 23:
Hassan M, Vanjare BD, Sim KY, Raza H, Lee KH, Shahzadi S, Kloczkowski A. Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase. Molecules. 2022 Mar 7; 27:
Li MS, Kloczkowski A, Cieplak M, Kouza M. Final Remarks. Methods Mol Biol. 2022; 2340: 469-470.
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol. 2022; 2340: 41-50.
Hassan M, Iqbal MS, Naqvi S, Alashwal H, Moustafa AA, Kloczkowski A. Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches. Front Mol Biosci. 2022; 9: 866072.
Hassan M, Zahid S, Alashwal H, Kloczkowski A, Moustafa AA. Mechanistic insights into TNFR1/MADD death domains in Alzheimer's disease through conformational molecular dynamic analysis. Sci Rep. 2021 Jun 10; 11: 12256.
Agrawal S, Ransom RF, Saraswathi S, Garcia-Gonzalo E, Webb A, Fernandez-Martinez JL, Popovic M, Guess AJ, Kloczkowski A, Benndorf R, Sadee W, Smoyer WE, On Behalf Of The Pediatric Nephrology Research Consortium Pnrc. Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. J Clin Med. 2021 Feb 2; 10:
Fernández-Martínez JL, Fernández-Muñiz Z, Cernea A, Kloczkowski A. Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic. Comput Math Methods Med. 2021; 2021: 5556433.
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 2021 Jan 8; 49: D298-D308.
Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods Mol Biol. 2021; 2190: 307-316.
Álvarez-Machancoses Ó, Fernández-Martínez JL, Kloczkowski A. Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules. 2020 May 26; 25:
Fernández-Martínez JL, Álvarez-Machancoses Ó, de Andrés-Galiana EJ, Bea G, Kloczkowski A. Robust Sampling of Defective Pathways in Alzheimer's Disease. Implications in Drug Repositioning. Int J Mol Sci. 2020 May 19; 21:
Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci. 2020; 7: 607323.
Alterovitz WL, Faraggi E, Oldfield CJ, Meng J, Xue B, Huang F, Romero P, Kloczkowski A, Uversky VN, Dunker AK. Many-to-one binding by intrinsically disordered protein regions. Pac Symp Biocomput. 2020; 25: 159-170.
Álvarez-Machancoses Ó, De Andrés-Galiana EJ, Fernández-Martínez JL, Kloczkowski A. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. Biomolecules. 2019 Dec 31; 10:
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci. 2019 Sep 21; 20:
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel). 2019 Aug; 21:
Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model. 2019 Feb 27; 25: 79.
Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel). 2018 Dec 3; 9:
Lan PD, Kouza M, Kloczkowski A, Li MS. A topological order parameter for describing folding free energy landscapes of proteins. J Chem Phys. 2018 Nov 7; 149: 175101.
Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci. 2018 Nov 6; 19:
Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules. 2018 Aug 10; 23:
Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn. 2018 Jul; 36: 2331-2341.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Gieldon A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Slusarz M, Slusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popovic Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Oldziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Foldit Players consortium., Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018 Jul 2; 8: 9939.
Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys. 2018 Jun 7; 148: 215106.
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol. 2018 Apr; 16: 1850005.
View More Publications
Research
Lab(s)
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Publications
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120: e2214423119.
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules. 2023 Jan 3; 28:
Hassan M, Shahzadi S, Kloczkowski A. Tyrosinase Inhibitors Naturally Present in Plants and Synthetic Modifications of These Natural Products as Anti-Melanogenic Agents: A Review. Molecules. 2023 Jan 2; 28:
Hassan M, Amir A, Shahzadi S, Kloczkowski A. Therapeutic Implications of microRNAs in Depressive Disorders: A Review. Int J Mol Sci. 2022 Nov 4; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Álvarez-Machancoses Ó, Bea G, Galmarini CM, Kloczkowski A. Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput Biol Med. 2022 Oct; 149: 106029.
Hosseini Nasab N, Raza H, Shim RS, Hassan M, Kloczkowski A, Kim SJ. Potent Alkaline Phosphatase Inhibitors, Pyrazolo-Oxothiazolidines: Synthesis, Biological Evaluation, Molecular Docking, and Kinetic Studies. Int J Mol Sci. 2022 Oct 31; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Fernández-Brillet L, Cernea A, Kloczkowski A. Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space. Int J Mol Sci. 2022 Oct 26; 23:
Irfan A, Zahoor AF, Kamal S, Hassan M, Kloczkowski A. Ultrasonic-Assisted Synthesis of Benzofuran Appended Oxadiazole Molecules as Tyrosinase Inhibitors: Mechanistic Approach through Enzyme Inhibition, Molecular Docking, Chemoinformatics, ADMET and Drug-Likeness Studies. Int J Mol Sci. 2022 Sep 19; 23:
Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS Omega. 2022 Jun 14; 7: 19243-19260.
Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci. 2022 Jun 30; 23:
Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci. 2022 Apr 22; 23:
Hassan M, Vanjare BD, Sim KY, Raza H, Lee KH, Shahzadi S, Kloczkowski A. Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase. Molecules. 2022 Mar 7; 27:
Li MS, Kloczkowski A, Cieplak M, Kouza M. Final Remarks. Methods Mol Biol. 2022; 2340: 469-470.
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol. 2022; 2340: 41-50.
Hassan M, Iqbal MS, Naqvi S, Alashwal H, Moustafa AA, Kloczkowski A. Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches. Front Mol Biosci. 2022; 9: 866072.
Hassan M, Zahid S, Alashwal H, Kloczkowski A, Moustafa AA. Mechanistic insights into TNFR1/MADD death domains in Alzheimer's disease through conformational molecular dynamic analysis. Sci Rep. 2021 Jun 10; 11: 12256.
Agrawal S, Ransom RF, Saraswathi S, Garcia-Gonzalo E, Webb A, Fernandez-Martinez JL, Popovic M, Guess AJ, Kloczkowski A, Benndorf R, Sadee W, Smoyer WE, On Behalf Of The Pediatric Nephrology Research Consortium Pnrc. Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. J Clin Med. 2021 Feb 2; 10:
Fernández-Martínez JL, Fernández-Muñiz Z, Cernea A, Kloczkowski A. Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic. Comput Math Methods Med. 2021; 2021: 5556433.
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 2021 Jan 8; 49: D298-D308.
Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods Mol Biol. 2021; 2190: 307-316.
Álvarez-Machancoses Ó, Fernández-Martínez JL, Kloczkowski A. Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules. 2020 May 26; 25:
Fernández-Martínez JL, Álvarez-Machancoses Ó, de Andrés-Galiana EJ, Bea G, Kloczkowski A. Robust Sampling of Defective Pathways in Alzheimer's Disease. Implications in Drug Repositioning. Int J Mol Sci. 2020 May 19; 21:
Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci. 2020; 7: 607323.
Alterovitz WL, Faraggi E, Oldfield CJ, Meng J, Xue B, Huang F, Romero P, Kloczkowski A, Uversky VN, Dunker AK. Many-to-one binding by intrinsically disordered protein regions. Pac Symp Biocomput. 2020; 25: 159-170.
Álvarez-Machancoses Ó, De Andrés-Galiana EJ, Fernández-Martínez JL, Kloczkowski A. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. Biomolecules. 2019 Dec 31; 10:
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci. 2019 Sep 21; 20:
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel). 2019 Aug; 21:
Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model. 2019 Feb 27; 25: 79.
Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel). 2018 Dec 3; 9:
Lan PD, Kouza M, Kloczkowski A, Li MS. A topological order parameter for describing folding free energy landscapes of proteins. J Chem Phys. 2018 Nov 7; 149: 175101.
Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci. 2018 Nov 6; 19:
Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules. 2018 Aug 10; 23:
Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn. 2018 Jul; 36: 2331-2341.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Gieldon A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Slusarz M, Slusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popovic Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Oldziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Foldit Players consortium., Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018 Jul 2; 8: 9939.
Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys. 2018 Jun 7; 148: 215106.
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol. 2018 Apr; 16: 1850005.
View More Publications
Lab(s)
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Publications
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120: e2214423119.
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules. 2023 Jan 3; 28:
Hassan M, Shahzadi S, Kloczkowski A. Tyrosinase Inhibitors Naturally Present in Plants and Synthetic Modifications of These Natural Products as Anti-Melanogenic Agents: A Review. Molecules. 2023 Jan 2; 28:
Hassan M, Amir A, Shahzadi S, Kloczkowski A. Therapeutic Implications of microRNAs in Depressive Disorders: A Review. Int J Mol Sci. 2022 Nov 4; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Álvarez-Machancoses Ó, Bea G, Galmarini CM, Kloczkowski A. Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput Biol Med. 2022 Oct; 149: 106029.
Hosseini Nasab N, Raza H, Shim RS, Hassan M, Kloczkowski A, Kim SJ. Potent Alkaline Phosphatase Inhibitors, Pyrazolo-Oxothiazolidines: Synthesis, Biological Evaluation, Molecular Docking, and Kinetic Studies. Int J Mol Sci. 2022 Oct 31; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Fernández-Brillet L, Cernea A, Kloczkowski A. Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space. Int J Mol Sci. 2022 Oct 26; 23:
Irfan A, Zahoor AF, Kamal S, Hassan M, Kloczkowski A. Ultrasonic-Assisted Synthesis of Benzofuran Appended Oxadiazole Molecules as Tyrosinase Inhibitors: Mechanistic Approach through Enzyme Inhibition, Molecular Docking, Chemoinformatics, ADMET and Drug-Likeness Studies. Int J Mol Sci. 2022 Sep 19; 23:
Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS Omega. 2022 Jun 14; 7: 19243-19260.
Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci. 2022 Jun 30; 23:
Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci. 2022 Apr 22; 23:
Hassan M, Vanjare BD, Sim KY, Raza H, Lee KH, Shahzadi S, Kloczkowski A. Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase. Molecules. 2022 Mar 7; 27:
Li MS, Kloczkowski A, Cieplak M, Kouza M. Final Remarks. Methods Mol Biol. 2022; 2340: 469-470.
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol. 2022; 2340: 41-50.
Hassan M, Iqbal MS, Naqvi S, Alashwal H, Moustafa AA, Kloczkowski A. Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches. Front Mol Biosci. 2022; 9: 866072.
Hassan M, Zahid S, Alashwal H, Kloczkowski A, Moustafa AA. Mechanistic insights into TNFR1/MADD death domains in Alzheimer's disease through conformational molecular dynamic analysis. Sci Rep. 2021 Jun 10; 11: 12256.
Agrawal S, Ransom RF, Saraswathi S, Garcia-Gonzalo E, Webb A, Fernandez-Martinez JL, Popovic M, Guess AJ, Kloczkowski A, Benndorf R, Sadee W, Smoyer WE, On Behalf Of The Pediatric Nephrology Research Consortium Pnrc. Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. J Clin Med. 2021 Feb 2; 10:
Fernández-Martínez JL, Fernández-Muñiz Z, Cernea A, Kloczkowski A. Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic. Comput Math Methods Med. 2021; 2021: 5556433.
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 2021 Jan 8; 49: D298-D308.
Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods Mol Biol. 2021; 2190: 307-316.
Álvarez-Machancoses Ó, Fernández-Martínez JL, Kloczkowski A. Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules. 2020 May 26; 25:
Fernández-Martínez JL, Álvarez-Machancoses Ó, de Andrés-Galiana EJ, Bea G, Kloczkowski A. Robust Sampling of Defective Pathways in Alzheimer's Disease. Implications in Drug Repositioning. Int J Mol Sci. 2020 May 19; 21:
Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci. 2020; 7: 607323.
Alterovitz WL, Faraggi E, Oldfield CJ, Meng J, Xue B, Huang F, Romero P, Kloczkowski A, Uversky VN, Dunker AK. Many-to-one binding by intrinsically disordered protein regions. Pac Symp Biocomput. 2020; 25: 159-170.
Álvarez-Machancoses Ó, De Andrés-Galiana EJ, Fernández-Martínez JL, Kloczkowski A. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. Biomolecules. 2019 Dec 31; 10:
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci. 2019 Sep 21; 20:
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel). 2019 Aug; 21:
Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model. 2019 Feb 27; 25: 79.
Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel). 2018 Dec 3; 9:
Lan PD, Kouza M, Kloczkowski A, Li MS. A topological order parameter for describing folding free energy landscapes of proteins. J Chem Phys. 2018 Nov 7; 149: 175101.
Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci. 2018 Nov 6; 19:
Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules. 2018 Aug 10; 23:
Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn. 2018 Jul; 36: 2331-2341.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Gieldon A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Slusarz M, Slusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popovic Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Oldziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Foldit Players consortium., Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018 Jul 2; 8: 9939.
Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys. 2018 Jun 7; 148: 215106.
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol. 2018 Apr; 16: 1850005.
View More Publications
Lab(s)
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120: e2214423119.
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules. 2023 Jan 3; 28:
Hassan M, Shahzadi S, Kloczkowski A. Tyrosinase Inhibitors Naturally Present in Plants and Synthetic Modifications of These Natural Products as Anti-Melanogenic Agents: A Review. Molecules. 2023 Jan 2; 28:
Hassan M, Amir A, Shahzadi S, Kloczkowski A. Therapeutic Implications of microRNAs in Depressive Disorders: A Review. Int J Mol Sci. 2022 Nov 4; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Álvarez-Machancoses Ó, Bea G, Galmarini CM, Kloczkowski A. Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput Biol Med. 2022 Oct; 149: 106029.
Hosseini Nasab N, Raza H, Shim RS, Hassan M, Kloczkowski A, Kim SJ. Potent Alkaline Phosphatase Inhibitors, Pyrazolo-Oxothiazolidines: Synthesis, Biological Evaluation, Molecular Docking, and Kinetic Studies. Int J Mol Sci. 2022 Oct 31; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Fernández-Brillet L, Cernea A, Kloczkowski A. Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space. Int J Mol Sci. 2022 Oct 26; 23:
Irfan A, Zahoor AF, Kamal S, Hassan M, Kloczkowski A. Ultrasonic-Assisted Synthesis of Benzofuran Appended Oxadiazole Molecules as Tyrosinase Inhibitors: Mechanistic Approach through Enzyme Inhibition, Molecular Docking, Chemoinformatics, ADMET and Drug-Likeness Studies. Int J Mol Sci. 2022 Sep 19; 23:
Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS Omega. 2022 Jun 14; 7: 19243-19260.
Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci. 2022 Jun 30; 23:
Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci. 2022 Apr 22; 23:
Hassan M, Vanjare BD, Sim KY, Raza H, Lee KH, Shahzadi S, Kloczkowski A. Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase. Molecules. 2022 Mar 7; 27:
Li MS, Kloczkowski A, Cieplak M, Kouza M. Final Remarks. Methods Mol Biol. 2022; 2340: 469-470.
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol. 2022; 2340: 41-50.
Hassan M, Iqbal MS, Naqvi S, Alashwal H, Moustafa AA, Kloczkowski A. Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches. Front Mol Biosci. 2022; 9: 866072.
Hassan M, Zahid S, Alashwal H, Kloczkowski A, Moustafa AA. Mechanistic insights into TNFR1/MADD death domains in Alzheimer's disease through conformational molecular dynamic analysis. Sci Rep. 2021 Jun 10; 11: 12256.
Agrawal S, Ransom RF, Saraswathi S, Garcia-Gonzalo E, Webb A, Fernandez-Martinez JL, Popovic M, Guess AJ, Kloczkowski A, Benndorf R, Sadee W, Smoyer WE, On Behalf Of The Pediatric Nephrology Research Consortium Pnrc. Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. J Clin Med. 2021 Feb 2; 10:
Fernández-Martínez JL, Fernández-Muñiz Z, Cernea A, Kloczkowski A. Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic. Comput Math Methods Med. 2021; 2021: 5556433.
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 2021 Jan 8; 49: D298-D308.
Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods Mol Biol. 2021; 2190: 307-316.
Álvarez-Machancoses Ó, Fernández-Martínez JL, Kloczkowski A. Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules. 2020 May 26; 25:
Fernández-Martínez JL, Álvarez-Machancoses Ó, de Andrés-Galiana EJ, Bea G, Kloczkowski A. Robust Sampling of Defective Pathways in Alzheimer's Disease. Implications in Drug Repositioning. Int J Mol Sci. 2020 May 19; 21:
Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci. 2020; 7: 607323.
Alterovitz WL, Faraggi E, Oldfield CJ, Meng J, Xue B, Huang F, Romero P, Kloczkowski A, Uversky VN, Dunker AK. Many-to-one binding by intrinsically disordered protein regions. Pac Symp Biocomput. 2020; 25: 159-170.
Álvarez-Machancoses Ó, De Andrés-Galiana EJ, Fernández-Martínez JL, Kloczkowski A. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. Biomolecules. 2019 Dec 31; 10:
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci. 2019 Sep 21; 20:
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel). 2019 Aug; 21:
Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model. 2019 Feb 27; 25: 79.
Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel). 2018 Dec 3; 9:
Lan PD, Kouza M, Kloczkowski A, Li MS. A topological order parameter for describing folding free energy landscapes of proteins. J Chem Phys. 2018 Nov 7; 149: 175101.
Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci. 2018 Nov 6; 19:
Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules. 2018 Aug 10; 23:
Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn. 2018 Jul; 36: 2331-2341.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Gieldon A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Slusarz M, Slusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popovic Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Oldziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Foldit Players consortium., Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018 Jul 2; 8: 9939.
Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys. 2018 Jun 7; 148: 215106.
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol. 2018 Apr; 16: 1850005.
View More Publications
Lab(s)
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Battelle Center for Mathematical Medicine
Kloczkowski Lab
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120: e2214423119.
Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. Molecules. 2023 Jan 3; 28:
Hassan M, Shahzadi S, Kloczkowski A. Tyrosinase Inhibitors Naturally Present in Plants and Synthetic Modifications of These Natural Products as Anti-Melanogenic Agents: A Review. Molecules. 2023 Jan 2; 28:
Hassan M, Amir A, Shahzadi S, Kloczkowski A. Therapeutic Implications of microRNAs in Depressive Disorders: A Review. Int J Mol Sci. 2022 Nov 4; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Álvarez-Machancoses Ó, Bea G, Galmarini CM, Kloczkowski A. Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput Biol Med. 2022 Oct; 149: 106029.
Hosseini Nasab N, Raza H, Shim RS, Hassan M, Kloczkowski A, Kim SJ. Potent Alkaline Phosphatase Inhibitors, Pyrazolo-Oxothiazolidines: Synthesis, Biological Evaluation, Molecular Docking, and Kinetic Studies. Int J Mol Sci. 2022 Oct 31; 23:
deAndrés-Galiana EJ, Fernández-Martínez JL, Fernández-Brillet L, Cernea A, Kloczkowski A. Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space. Int J Mol Sci. 2022 Oct 26; 23:
Irfan A, Zahoor AF, Kamal S, Hassan M, Kloczkowski A. Ultrasonic-Assisted Synthesis of Benzofuran Appended Oxadiazole Molecules as Tyrosinase Inhibitors: Mechanistic Approach through Enzyme Inhibition, Molecular Docking, Chemoinformatics, ADMET and Drug-Likeness Studies. Int J Mol Sci. 2022 Sep 19; 23:
Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS Omega. 2022 Jun 14; 7: 19243-19260.
Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci. 2022 Jun 30; 23:
Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci. 2022 Apr 22; 23:
Hassan M, Vanjare BD, Sim KY, Raza H, Lee KH, Shahzadi S, Kloczkowski A. Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase. Molecules. 2022 Mar 7; 27:
Li MS, Kloczkowski A, Cieplak M, Kouza M. Final Remarks. Methods Mol Biol. 2022; 2340: 469-470.
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods Mol Biol. 2022; 2340: 41-50.
Hassan M, Iqbal MS, Naqvi S, Alashwal H, Moustafa AA, Kloczkowski A. Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches. Front Mol Biosci. 2022; 9: 866072.
Hassan M, Zahid S, Alashwal H, Kloczkowski A, Moustafa AA. Mechanistic insights into TNFR1/MADD death domains in Alzheimer’s disease through conformational molecular dynamic analysis. Sci Rep. 2021 Jun 10; 11: 12256.
Agrawal S, Ransom RF, Saraswathi S, Garcia-Gonzalo E, Webb A, Fernandez-Martinez JL, Popovic M, Guess AJ, Kloczkowski A, Benndorf R, Sadee W, Smoyer WE, On Behalf Of The Pediatric Nephrology Research Consortium Pnrc. Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. J Clin Med. 2021 Feb 2; 10:
Fernández-Martínez JL, Fernández-Muñiz Z, Cernea A, Kloczkowski A. Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic. Comput Math Methods Med. 2021; 2021: 5556433.
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 2021 Jan 8; 49: D298-D308.
Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods Mol Biol. 2021; 2190: 307-316.
Álvarez-Machancoses Ó, Fernández-Martínez JL, Kloczkowski A. Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. Molecules. 2020 May 26; 25:
Fernández-Martínez JL, Álvarez-Machancoses Ó, de Andrés-Galiana EJ, Bea G, Kloczkowski A. Robust Sampling of Defective Pathways in Alzheimer’s Disease. Implications in Drug Repositioning. Int J Mol Sci. 2020 May 19; 21:
Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci. 2020; 7: 607323.
Alterovitz WL, Faraggi E, Oldfield CJ, Meng J, Xue B, Huang F, Romero P, Kloczkowski A, Uversky VN, Dunker AK. Many-to-one binding by intrinsically disordered protein regions. Pac Symp Biocomput. 2020; 25: 159-170.
Álvarez-Machancoses Ó, De Andrés-Galiana EJ, Fernández-Martínez JL, Kloczkowski A. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. Biomolecules. 2019 Dec 31; 10:
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci. 2019 Sep 21; 20:
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel). 2019 Aug; 21:
Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model. 2019 Feb 27; 25: 79.
Faraggi E, Krupa P, Mozolewska MA, Liwo A, Kloczkowski A. Reoptimized UNRES Potential for Protein Model Quality Assessment. Genes (Basel). 2018 Dec 3; 9:
Lan PD, Kouza M, Kloczkowski A, Li MS. A topological order parameter for describing folding free energy landscapes of proteins. J Chem Phys. 2018 Nov 7; 149: 175101.
Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci. 2018 Nov 6; 19:
Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules. 2018 Aug 10; 23:
Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn. 2018 Jul; 36: 2331-2341.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Gieldon A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Slusarz M, Slusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popovic Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Oldziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Foldit Players consortium., Crivelli SN. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018 Jul 2; 8: 9939.
Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys. 2018 Jun 7; 148: 215106.
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol. 2018 Apr; 16: 1850005.
Biography
Andrzej Kloczkowski is Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He is a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski’s NIH-funded research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
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See Andrzej Kloczkowski’s Curriculum Vitae (CV)
Biography
Andrzej Kloczkowski is Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He is a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski’s NIH-funded research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
View My Publications Connect on LinkedIn Connect on Google Scholar
See Andrzej Kloczkowski’s Curriculum Vitae (CV)
Biography
Andrzej Kloczkowski is Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He is a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski’s NIH-funded research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
View My Publications Connect on LinkedIn Connect on Google Scholar
See Andrzej Kloczkowski’s Curriculum Vitae (CV)
Andrzej Kloczkowski is Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He is a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski’s NIH-funded research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
View My Publications Connect on LinkedIn Connect on Google Scholar
See Andrzej Kloczkowski’s Curriculum Vitae (CV)
Andrzej Kloczkowski is Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He is a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski’s NIH-funded research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
- View My Publications
- Connect on LinkedIn
- Connect on Google Scholar
See Andrzej Kloczkowski’s Curriculum Vitae (CV)
Academic and Clinical Areas
Battelle Center for Mathematical Medicine
Faculty
Kloczkowski Lab
Principal Investigator
Primary Department
Battelle Center for Mathematical Medicine
Academic and Clinical Areas
Battelle Center for Mathematical Medicine
Faculty
Kloczkowski Lab
Principal Investigator
Primary Department
Battelle Center for Mathematical Medicine
Academic and Clinical Areas
Battelle Center for Mathematical Medicine
Faculty
Kloczkowski Lab
Principal Investigator
Primary Department
Battelle Center for Mathematical Medicine
Battelle Center for Mathematical Medicine
Faculty
Kloczkowski Lab
Principal Investigator
Primary Department
Battelle Center for Mathematical Medicine
- Battelle Center for Mathematical Medicine
- Faculty
- Kloczkowski Lab
- Principal Investigator
- Primary Department
- Battelle Center for Mathematical Medicine
Professional Experience
2010 - Present Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Principal Investigator,2007 - 2010 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist II2005 - 2010 Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Adjunct (Full) Professor2002 - 2007 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist I
Professional Experience
2010 - Present Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Principal Investigator,2007 - 2010 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist II2005 - 2010 Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Adjunct (Full) Professor2002 - 2007 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist I
Professional Experience
2010 - Present Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Principal Investigator,2007 - 2010 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist II2005 - 2010 Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Adjunct (Full) Professor2002 - 2007 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist I
2010 - Present Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Principal Investigator,2007 - 2010 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist II2005 - 2010 Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Adjunct (Full) Professor2002 - 2007 Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Scientist I
2010 - Present Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Principal Investigator,
Contact Information
Battelle Center for Mathematical Medicine
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski
Abigail Wexner Research Institute700 Children's DriveColumbus, Ohio 43205 (map)
Contact Information
Battelle Center for Mathematical Medicine
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski
Abigail Wexner Research Institute700 Children's DriveColumbus, Ohio 43205 (map)
Contact Information
Battelle Center for Mathematical Medicine
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski
Abigail Wexner Research Institute700 Children's DriveColumbus, Ohio 43205 (map)
Battelle Center for Mathematical Medicine
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski
Abigail Wexner Research Institute700 Children's DriveColumbus, Ohio 43205 (map)
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski
Abigail Wexner Research Institute700 Children's DriveColumbus, Ohio 43205 (map)
Call us at: (614)355-5622
Fax us at: (614) 355-6671
Email Andrzej Kloczkowski
Abigail Wexner Research Institute700 Children's DriveColumbus, Ohio 43205 (map)
- Call us at:
- (614)355-5622
- Fax us at:
- (614) 355-6671
- Email Andrzej Kloczkowski
- Abigail Wexner Research Institute700 Children’s DriveColumbus, Ohio 43205 (map)
