Filters: Author is Brylinski, Michal [Clear All Filters]
Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures. The Journal of Physical Chemistry B. 116(23):6654-6664. PDF. 2012.
FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins: Structure, Function, and Bioinformatics. 79(3):735-751. PDF. 2011.
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. Journal of Structural Biology. 173(3):558-569. PDF. 2011.
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function Physical Chemistry Chemical Physics. 13 (38):17044-17055. PDF. 2011.
PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (Oxford, England). 26(5):687-8. PDF. 2010.
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. Journal of computational chemistry. 31(5):1093-105. PDF. 2010.
Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach. Molecular Pharmaceutics. 7(6):2324–2333. PDF. 2010.
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. Journal of Chemical Information and Modeling. 50:1839-1854. PDF. 2010.
The continuity of protein structure space is an intrinsic property of proteins. Proceedings of the National Academy of Sciences of the United States of America. 106(37):15690-5. PDF. 2009.
FINDSITE: a threading-based approach to ligand homology modeling. PLoS computational biology. 5(6):e1000405. PDF. 2009.
FINDSITE: a combined evolution/structure-based approach to protein function prediction. Briefings in bioinformatics. 10(4):378-91. PDF. 2009.
Active site recognition in silico. Structure-function relation in proteins. 1:105-127.. 2009.
Folding process in the presence of specific ligand. Structure-function relation in proteins. 1:129-148.. 2009.
Late-stage folding intermediate in silico model. Structure-function relation in proteins. 1:79-103.. 2009.
Reply to Zimmerman et al: The space of single domain protein structures is continuous and highly connected. Proc Natl Acad Science 2009:106(51): E138. PDF. 2009.
Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family. Journal of theoretical biology. 251(2):275-85. PDF. 2008.
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. Journal of computational chemistry. 29(10):1574-88. PDF Supplementary Data. 2008.
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proceedings of the National Academy of Sciences of the United States of America. 105(1):129-34. PDF Supplementary Data. 2008.
What is the relationship between the global structures of apo and holo proteins? Proteins. 70(2):363-77. PDF Supplementary Data. 2008.
Prediction of functional sites based on the fuzzy oil drop model. PLoS computational biology. 3(5):e94. PDF. 2007.
Localization of ligand binding site in proteins identified in silico. Journal of molecular modeling. 13(6-7):665-75. PDF. 2007.
Is the protein folding an aim-oriented process? Human haemoglobin as example International journal of bioinformatics research and applications. 3(2):234-60. PDF. 2007.
Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor. Biochimie. 88(9):1229-39. PDF. 2006.
A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. Medical science monitor : international medical journal of experimental and clinical research. 12(6):BR208-14. PDF. 2006.
Stereoselectivity of 8-OH-DPAT toward the serotonin 5-HT1A receptor: biochemical and molecular modeling study. Biochemical pharmacology. 72(4):498-511. PDF. 2006.
Hydrophobic collapse in (in silico) protein folding. Computational biology and chemistry. 30(4):255-67. PDF. 2006.
Fuzzy-oil-drop hydrophobic force field--a model to represent late-stage folding (in silico) of lysozyme. Journal of biomolecular structure & dynamics. 23(5):519-28. PDF. 2006.
Gauss-function-Based model of hydrophobicity density in proteins. In silico biology. 6(1-2):15-22. PDF. 2006.
Sequence-structure-function relation characterized in silico. In silico biology. 6(6):589-600. PDF. 2006.
Early-stage folding in proteins (in silico) sequence-to-structure relation. Journal of biomedicine & biotechnology. 2005(2):65-79. PDF. 2005.
SPI--structure predictability index for protein sequences.. In silico biology. 5(3):227-37. PDF. 2005.
Lysozyme folded in silico according to the limited conformational sub-space.. Journal of biomolecular structure & dynamics. 22(2):149-58. PDF. 2004.
Limited conformational space for early-stage protein folding simulation.. Bioinformatics (Oxford, England). 20(2):199-205. PDF. 2004.
Conformational subspace in simulation of early-stage protein folding.. Proteins. 55(1):115-27. PDF. 2004.