Deciphering common failures in molecular docking of ligand-protein complexes
Verkhivker, G M, Bouzida, D, Gehlhaar, D K, Rejto, P A, Arthurs, S, Colson, A B, Freer, S T, Larson, V, Luty, B A, Marrone, T, Rose, P W
Published in Journal of computer-aided molecular design (01.11.2000)
Published in Journal of computer-aided molecular design (01.11.2000)
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Journal Article
A Mean Field Model of Ligand-Protein Interactions: Implications for the Structural Assessment of Human Immunodeficiency Virus Type 1 Protease Complexes and Receptor-Specific Binding
Verkhivker, Gennady M., Rejto, Paul A.
Published in Proceedings of the National Academy of Sciences - PNAS (09.01.1996)
Published in Proceedings of the National Academy of Sciences - PNAS (09.01.1996)
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Journal Article
Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity
Rejto, Paul A., Verkhivker, Gennady M.
Published in Proteins, structure, function, and bioinformatics (01.07.1997)
Published in Proteins, structure, function, and bioinformatics (01.07.1997)
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Journal Article
Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: Structural analysis of the peptide complexes with SH2 domains
Verkhivker, Gennady M., Bouzida, Djamal, Gehlhaar, Daniel K., Rejto, Paul A., Schaffer, Lana, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose, Peter W.
Published in Proteins, structure, function, and bioinformatics (01.12.2001)
Published in Proteins, structure, function, and bioinformatics (01.12.2001)
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Journal Article
Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides
Verkhivker, Gennady M, Bouzida, Djamal, Gehlhaar, Daniel K, Rejto, Paul A, Schaffer, Lana, Arthurs, Sandra, Colson, Anthony B, Freer, Stephan T, Larson, Veda, Luty, Brock A, Marrone, Tami, Rose, Peter W
Published in Journal of medicinal chemistry (03.01.2002)
Published in Journal of medicinal chemistry (03.01.2002)
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Journal Article
Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions
Verkhivker, Gennady M., Rejto, Paul A., Bouzida, Djamal, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Gehlhaar, Daniel K., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose, Peter W.
Published in Journal of molecular recognition (01.11.1999)
Published in Journal of molecular recognition (01.11.1999)
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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
Gehlhaar, Daniel K., Verkhivker, Gennady M., Rejto, Paul A., Sherman, Christopher J., Fogel, David R., Fogel, Lawrence J., Freer, Stephan T.
Published in Chemistry & biology (01.05.1995)
Published in Chemistry & biology (01.05.1995)
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Journal Article
Simulating Disorder-Order Transitions in Molecular Recognition of Unstructured Proteins: Where Folding Meets Binding
Verkhivker, Gennady M., Bouzida, Djamal, Gehlhaar, Daniel K., Rejto, Paul A., Freer, Stephan T., Rose, Peter W.
Published in Proceedings of the National Academy of Sciences - PNAS (29.04.2003)
Published in Proceedings of the National Academy of Sciences - PNAS (29.04.2003)
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Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: Deciphering the effect of intermolecular interactions on computational structure prediction of the p27Kip1 protein bound to the cyclin A-cyclin-dependent kinase 2 complex
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Complexity and simplicity of ligand–macromolecule interactions: the energy landscape perspective
Verkhivker, Gennady M, Bouzida, Djamal, Gehlhaar, Daniel K, Rejto, Paul A, Freer, Stephan T, Rose, Peter W
Published in Current Opinion in Structural Biology (01.04.2002)
Published in Current Opinion in Structural Biology (01.04.2002)
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Book Review
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Empirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations
Verkhivker, G M
Published in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1996)
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Published in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1996)
Journal Article
Exploring the energy landscapes of molecular recognition by a genetic algorithm: analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes
Verkhivker, G M, Rejto, P A, Gehlhaar, D K, Freer, S T
Published in Proteins, structure, function, and bioinformatics (01.07.1996)
Published in Proteins, structure, function, and bioinformatics (01.07.1996)
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