D. Bouzida

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 .

THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

R. Swendsen, P. Kollman, D. Bouzida, 1992 .

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.

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.

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.

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 .

Structural modifications of a 3-methoxy-2-aminopyridine compound to reduce potential for mutagenicity and time-dependent drug-drug interaction.

D. Bouzida, M. Pairish, S. Yamazaki, 2012, Bioorganic & medicinal chemistry letters.

Identification of novel pyrrolopyrazoles as protein kinase C β II inhibitors.

D. Bouzida, Iriny Botrous, G. Alton, 2011, Bioorganic & medicinal chemistry letters.

Efficient pattern comparative method for selecting functionally important motifs in protein sequences: application to zinc enzymes.

T. Smith, I. Muchnik, A. Kister, 1993, Bio Systems.

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.

Deciphering common failures in molecular docking of ligand-protein complexes

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

Discovery of pyrroloaminopyrazoles as novel PAK inhibitors.

D. Bouzida, J. Christensen, R. Kania, 2012, Journal of medicinal chemistry.

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.

Multidimensional free‐energy calculations using the weighted histogram analysis method

Shankar Kumar, Peter A. Kollman, Robert H. Swendsen, 1995, J. Comput. Chem..

Monte Carlo study of the effect of β2‐microglobulin on the binding cleft of the HLA‐A2 complex

C. DeLisi, J. Garnier, J. Cornette, 1994, Protein science : a publication of the Protein Society.

Structure of the catalytic domain of human protein kinase C beta II complexed with a bisindolylmaleimide inhibitor.

Djamal Bouzida, D. Bouzida, N. Grodsky, 2006, Biochemistry.

MONTE CARLO STUDY OF LIGAND-PROTEIN BINDING ENERGY LANDSCAPES WITH THE WEIGHTED HISTOGRAM ANALYSIS METHOD

Paul A. Rejto, Djamal Bouzida, Gennady M Verkhivker, 1999 .

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.

Fully Automated and Rapic Flexible Docking of Inhibitors Covalently Bound to Serine Proteases

Paul A. Rejto, Daniel K. Gehlhaar, Djamal Bouzida, 1998, Evolutionary Programming.

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

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

Reduced Dimensionality in Ligand—Protein Structure Prediction: Covalent Inhibitors of Serine Proteases and Design of Site-Directed Combinatorial Libraries

Paul A. Rejto, Daniel K. Gehlhaar, Djamal Bouzida, 1999 .

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 .

Easy Does It: Reducing Complexity in Ligand-Protein Docking

Paul A. Rejto, Daniel K. Gehlhaar, Djamal Bouzida, 2000 .

Examining ligand-protein interactions with binding-energy landscapes

Paul A. Rejto, Djamal Bouzida, Gennady M Verkhivker, 1999 .

Molecular replacement by evolutionary search.

Barry F. Smith, B A Smith, C R Kissinger, 2001, Acta crystallographica. Section D, Biological crystallography.