Assistant Professor

Ph.D., Jagiellonian University, 20064443424140393837363534333231302928272625242322212019181716151413121110987654321

E-mail: michal@brylinski.org

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Research Interests

• Systems Biology, Chemical Systems Biology and Cheminformatics
• Drug discovery and design
• Ligand docking/screening
• Ligand comparative modeling
• Protein function inference
• Protein structure prediction
• Protein evolution
• High-performance computing
• Engineering and simulation of life

Publications

• 44. Brylinski M, Feinstein WP.  Submitted.  eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands.
• 43. Brylinski M.  Submitted.  eVolver: An optimization engine for evolving protein sequences to stabilize the respective structures.
• 42. Brylinski M.  2013.  The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol. 328:77-88.
• 41. Skolnick J, Zhou H, Brylinski M.  2012.  Further evidence for the likely completeness of the library of solved single domain protein structures. J Phys Chem B. 116(23):6654-64.
• 40. Brylinski M, Lingam D.  2012.  eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE. 7(11):e50200.
• 39. Brylinski M, Feinstein WP.  2012.  Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol. 6(1):001-010.
• 38. Brylinski M, Gao M, Skolnick J.  2011.  Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function Phys Chem Chem Phys. 13(38):17044-55.
• 37. Brylinski M, Skolnick J.  2011.  FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins. 79(3):735-51.
• 36. Brylinski M, Lee SY, Zhou H, Skolnick J.  2011.  The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. J Struct Biol. 173(3):558-69.
• 35. Brylinski M, Skolnick J.  2010.  Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. J Chem Inf Model. 50(10):1839-54.
• 34. Pandit SB, Brylinski M, Zhou H, Gao M, Arakaki AK, Skolnick J.  2010.  PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics. 26(5):687-8.
• 33. Brylinski M, Skolnick J.  2010.  Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins. 78(1):118-34.
• 32. Brylinski M, Skolnick J.  2010.  Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach. Mol Pharm. 7(6):2324-33.
• 31. Brylinski M, Skolnick J.  2010.  Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. J Comput Chem. 31(5):1093-105.
• 30. Skolnick J, Arakaki AK, Lee SY, Brylinski M.  2009.  The continuity of protein structure space is an intrinsic property of proteins. Proc Natl Acad Sci USA. 106(37):15690-5.
• 29. Brylinski M, Skolnick J.  2009.  FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput Biol. 5(6):e1000405.
• 28. Skolnick J, Brylinski M.  2009.  FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform. 10(4):378-91.
• 27. Brylinski M, Skolnick J.  2009.  Novel computational approaches to drug discovery. Proc Int Conf Quant Bio Inform. III:327-36.
• 26. Skolnick J, Lee SY, Brylinski M.  2009.  Reply to Zimmerman et al: The space of single domain protein structures is continuous and highly connected. Proc Natl Acad Sci USA. 106(51):E138.
• 25. Roterman I, Brylinski M, Konieczny L.  2009.  Active site recognition in silico. Structure-function relation in proteins. :105-27.
• 24. Roterman I, Konieczny L, Brylinski M.  2009.  Folding process in the presence of specific ligand. Structure-function relation in proteins. :129-48.
• 23. Roterman I, Konieczny L, Brylinski M.  2009.  Late-stage folding intermediate in silico model. Structure-function relation in proteins. :79-103.
• 22. Brylinski M, Konieczny L, Kononowicz A, Roterman I.  2008.  Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family. J Theor Biol. 251(2):275-85.
• 21. Brylinski M, Skolnick J.  2008.  Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J Comput Chem. 29(10):1574-88.
• 20. Brylinski M, Skolnick J.  2008.  A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci USA. 105(1):129-34.
• 19. Brylinski M, Skolnick J.  2008.  What is the relationship between the global structures of apo and holo proteins? Proteins. 70(2):363-77.
• 18. Brylinski M, Prymula K, Jurkowski W, Kochanczyk M, Stawowczyk E, Konieczny L, Roterman I.  2007.  Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol. 3(5):e94.
• 17. Brylinski M, Kochanczyk M, Broniatowska E, Roterman I.  2007.  Localization of ligand binding site in proteins identified in silico. J Mol Model. 13(6-7):665-75.
• 16. Brylinski M, Konieczny L, Roterman I.  2007.  Early-stage protein folding - In silico model. Recent Advances in Structural Bioinformatics. :69-104.
• 15. Brylinski M, Konieczny L, Roterman I.  2007.  Is the protein folding an aim-oriented process? Human haemoglobin as example. Int J Bioinform Res Appl. 3(2):234-60.
• 14. Brylinski M, Konieczny L, Roterman I.  2006.  Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor. Biochimie. 88(9):1229-39.
• 13. Meus J, Brylinski M, Piwowar M, Piwowar P, Wiśniowski Z, Stefaniak J, Konieczny L, Surówka G, Roterman I.  2006.  A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. Med Sci Monit. 12(6):BR208-14.
• 12. Dabrowska J, Brylinski M.  2006.  Stereoselectivity of 8-OH-DPAT toward the serotonin 5-HT1A receptor: biochemical and molecular modeling study. Biochem Pharmacol. 72(4):498-511.
• 11. Brylinski M, Konieczny L, Roterman I.  2006.  Hydrophobic collapse in (in silico) protein folding. Comput Biol Chem. 30(4):255-67.
• 10. Brylinski M, Konieczny L, Roterman I.  2006.  Fuzzy-oil-drop hydrophobic force field - a model to represent late-stage folding (in silico) of lysozyme. J Biomol Struct Dyn. 23(5):519-28.
• 9. Konieczny L, Brylinski M, Roterman I.  2006.  Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol. 6(1-2):15-22.
• 8. Brylinski M, Konieczny L, Roterman I.  2006.  Ligation site in proteins recognized in silico. Bioinformation. 1(4):127-9.
• 7. Brylinski M, Kochanczyk M, Konieczny L, Roterman I.  2006.  Sequence-structure-function relation characterized in silico. In Silico Biol. 6(6):589-600.
• 6. Brylinski M, Konieczny L, Czerwonko P, Jurkowski W, Roterman I.  2005.  Early-stage folding in proteins (in silico) sequence-to-structure relation. J Biomed Biotechnol. 2005(2):65-79.
• 5. Brylinski M, Konieczny L, Roterman I.  2005.  SPI - structure predictability index for protein sequences. In Silico Biol. 5(3):227-37.
• 4. Jurkowski W, Brylinski M, Konieczny L, Roterman I.  2004.  Lysozyme folded in silico according to the limited conformational sub-space. J Biomol Struct Dyn. 22(2):149-58.
• 3. Brylinski M, Jurkowski W, Konieczny L, Roterman I.  2004.  Limited conformational space for early-stage protein folding simulation. Bioinformatics. 20(2):199-205.
• 2. Jurkowski W, Brylinski M, Konieczny L, Wiíniowski Z, Roterman I.  2004.  Conformational subspace in simulation of early-stage protein folding. Proteins. 55(1):115-27.
• 1. Jurkowski W, Brylinski M, Konieczny L, Roterman I.  2004.  Limitation of conformational space for proteins - early stage folding simulation of human α and β hemoglobin chains. TASK Quarterly. 8(3):413-22.