Georgia Institute of TechnologyCenter for the study of systems biology
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Dr. Michal Brylinski

Research Scientist II

Michal Brylinski
Michal Brylinski

    Contact information:
  • Center for the Study of Systems Biology
  • 250 14th Street NW, Room 110
  • Atlanta GA, 30318, Mail Code:0590
  • Tel :(404) 407-8984
  • Fax :(404) 385-7478
  • Email: mbrylinski3@mail.gatech.edu

Research Interests

I am generally interested in protein structure, folding and dynamics. The field of my scientific interests includes:

  • sequence-structure-function relationship in proteins
  • protein structure prediction
  • simulation of protein folding/unfolding
  • active site recognition
  • ligand automated docking
  • protein-protein interactions
  • drug discovery and design
  • modeling of proteins in a hydrophobic environment
  • molecular dynamics simulations of biomolecules

List of publications:

[27] Brylinski M, Skolnick J. (2009) Comparison of structure- and threading-based approaches to protein functional annotation. Proteins, in press.
[26] Skolnick J, Arakaki AK, Lee S, Brylinski M. (2009) The continuity of protein structure space is an intrinsic property of proteins. Proc Natl Acad Sci USA, in press.
[25] Brylinski M, Skolnick J. (2009) Q-DockLHM: Low-resolution refinement for ligand comparative modeling. J Comput Chem, in press.
[24] Skolnick J, Brylinski M. (2009) FINDSITE: A combined evolution/structure-based approach to protein function prediction. Briefings in Bioinformatics 10, 378-391.
[23] Brylinski M, Skolnick J. (2009) FINDSITELHM: A threading-based approach to ligand homology modeling. PLoS Comput Biol 5, e1000405.
[22] Brylinski M, Skolnick J. (2008) Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J Comput Chem 29, 1574-1588.
[21] Brylinski M, Skolnick J. (2008) FINDSITE: A threading-based method for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci USA 105, 129-134.
[20] Brylinski M, Konieczny L, Kononowicz A, Roterman I. (2008) Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpine family. J Theor Biol 251, 278-285.
[19] Brylinski M, Skolnick J. (2007) What is the relationship between the global structures of apo and holo proteins? Proteins 70, 363-77.
[18] Roterman I, Brylinski M, Konieczny L, Jurkowski W. (2007) Early-stage protein folding - In silico model. Recent Advances in Structural Biology 1, 69-104.
[17] 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, e94.
[16] Brylinski M, Kochanczyk M, Broniatowska E, Roterman I. (2007) Localization of ligand binding site in proteins identified in silico. J Mol Model 13, 665-675.
[15] Brylinski M, Konieczny L, Roterman I. (2006) Is the protein folding an aim-oriented process? Human haemoglobin as example. Int J Bioinf Res App 3, 234-260.
[14] Brylinski M, Kochanczyk M, Konieczny L, Roterman I. (2006) Sequence-structure-function relation characterized in silico. In Silico Biol 6, 589-600.
[13] Brylinski M, Konieczny L, Roterman I. (2006) Hydrophobic collapse in (in silico) protein folding. Comput Biol Chem 30, 255-67.
[12] 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, 519-28.
[11] Dabrowska J, Brylinski M. (2006) Stereoselectivity of 8-OH-DPAT toward the serotonin 5-HT1A receptor: biochemical and molecular modeling study. Biochem Pharmacol 72, 498-511.
[10] Brylinski M, Konieczny L, Roterman I. (2006) Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor. Biochimie 88, 1229-1239.
[9] Brylinski M, Konieczny L, Roterman I. (2006) Ligation site in proteins recognized in silico. Bioinformation 1, 127-9.
[8] Konieczny L, Brylinski M, Roterman I. (2006) Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol 6, 0002.
[7] Meus J, Brylinski M, Piwowar M, Piwowar P, Wisniowski Z, Stefaniak J, Konieczny L, Surowka 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, BR208-14.
[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 2, 65-79.
[5] Brylinski M, Jurkowski W, Konieczny L, Roterman I. (2004) Limited conformational space for early-stage protein folding simulation. Bioinformatics 20, 199-205.
[4] Brylinski M, Konieczny L, Roterman I. (2004) SPI - Structure predictability index for protein sequences. In Silico Biol 5, 0022.
[3] Jurkowski W, Brylinski M, Konieczny L, Wiiniowski Z, Roterman I. (2004) Conformational subspace in simulation of early-stage protein folding. Proteins 55, 115-27.
[2] 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, 149-58.
[1] Brylinski M, Jurkowski W, 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, 413-22.