S. Freer

发表

Computer simulations of ligand–protein binding with ensembles of protein conformations: A Monte Carlo study of HIV‐1 protease binding energy landscapes

Gennady M Verkhivker, B. Luty, D. Bouzida, 1999 .

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming.

Gennady M Verkhivker, D. Fogel, L. Fogel, 1995, Chemistry & biology.

Design of enzyme inhibitors using iterative protein crystallographic analysis.

S. Freer, C. Janson, K. Appelt, 1991, Journal of medicinal chemistry.

Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective.

Djamal Bouzida, Gennady M Verkhivker, Peter W Rose, 2002, Current opinion in structural biology.

Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: The energy landscape analysis of a hot spot at the intermolecular interface

Djamal Bouzida, Gennady M Verkhivker, Peter W Rose, 2002, Proteins.

Protein conformational substates from X-ray crystallography.

P. Rejto, S. Freer, P A Rejto, 1996, Progress in biophysics and molecular biology.

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand–protein interactions

Gennady M Verkhivker, D K Gehlhaar, D Bouzida, 1999, Journal of molecular recognition : JMR.

Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity.

Gennady M Verkhivker, S. Freer, K. Appelt, 1995, Protein engineering.

Computational detection of the binding‐site hot spot at the remodeled human growth hormone–receptor interface

Djamal Bouzida, Gennady M Verkhivker, Peter W Rose, 2003, Proteins.

De novo design of enzyme inhibitors by Monte Carlo ligand generation.

D K Gehlhaar, S. Freer, D. Gehlhaar, 1995, Journal of medicinal chemistry.

Chapter 8 – Monte Carlo simulations of HIV-1 protease binding dynamics and thermodynamics with ensembles of protein conformations: Incorporating protein flexibility in deciphering mechanisms of molecular recognition

Gennady M Verkhivker, B. Luty, D. Bouzida, 2001 .

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.

Gennady M Verkhivker, D K Gehlhaar, P. Rejto, 1996, Proteins.

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

Gennady M Verkhivker, P. Rejto, S. Freer, 1996 .

Docking Conformationally Flexible Small Molecules into a Protein Binding Site through Evolutionary Programming

David B. Fogel, Lawrence J. Fogel, Gennady Verkhivker, 1995, Evolutionary Programming.

X-ray crystallographic study of boronic acid adducts with subtilisin BPN' (Novo). A model for the catalytic transition state.

D. Matthews, J. Kraut, S. Freer, 1975, The Journal of biological chemistry.

Hierarchy of simulation models in predicting structure and energetics of the Src SH2 domain binding to tyrosyl phosphopeptides.

Gennady M Verkhivker, D. Bouzida, P. Rejto, 2002, Journal of medicinal chemistry.

Stereochemical mechanism of action for thymidylate synthase based on the X-ray structure of the covalent inhibitory ternary complex with 5-fluoro-2'-deoxyuridylate and 5,10-methylenetetrahydrofolate.

D. Matthews, S. Freer, C. Janson, 1990, Journal of molecular biology.

Deciphering common failures in molecular docking of ligand-protein complexes

Gennady Verkhivker, Peter W. Rose, Paul A. Rejto, 2000, J. Comput. Aided Mol. Des..

Simulating disorder–order transitions in molecular recognition of unstructured proteins: Where folding meets binding

Djamal Bouzida, Gennady M Verkhivker, Peter W Rose, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: Structural analysis of the peptide complexes with SH2 domains

Gennady M Verkhivker, D K Gehlhaar, D Bouzida, 2001, Proteins.

Parallel simulated tempering dynamics of ligand–protein binding with ensembles of protein conformations

Peter W. Rose, Paul A. Rejto, Daniel K. Gehlhaar, 2001 .

Navigating ligand–protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

Gennady M Verkhivker, B. Luty, D. Bouzida, 2001 .

Calculation of solvation and binding free energy differences for folate-based inhibitors of the enzyme thymidylate synthase

D. Matthews, S. Freer, D. Zichi, 1992 .

New trends in computational structure prediction of ligand-protein complexes for receptor-based drug design

Paul A. Rejto, Daniel K. Gehlhaar, Stephan T. Freer, 1997 .