Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

Long-Timescale Molecular-Dynamics Simulations of the Major Urinary Protein Provide Atomistic Interpretations of the Unusual Thermodynamics of Ligand Binding

(2010) Julie Roy et al.   BIOPHYSICAL JOURNAL

Computer-aided drug-discovery techniques that account for receptor flexibility

(2010) Jacob D Durrant et al.   CURRENT OPINION IN PHARMACOLOGY

Role of protein flexibility in the discovery of new drugs

(2010) Gloria Fuentes et al.   DRUG DEVELOPMENT RESEARCH

Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations

(2010) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

Effect of the Integration Method on the Accuracy and Computational Efficiency of Free Energy Calculations Using Thermodynamic Integration

(2010) Miguel Jorge et al.   Journal of Chemical Theory and Computation

A Displaced-Solvent Functional Analysis of Model Hydrophobic Enclosures

(2010) Robert Abel et al.   Journal of Chemical Theory and Computation

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

(2010) Jeff Wereszczynski et al.   Journal of Chemical Theory and Computation

Modeling Protein−Ligand Binding by Mining Minima

(2010) Wei Chen et al.   Journal of Chemical Theory and Computation

How Can Hydrophobic Association Be Enthalpy Driven?

(2010) Piotr Setny et al.   Journal of Chemical Theory and Computation

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

(2010) Wei Jiang et al.   Journal of Chemical Theory and Computation

Water in Cavity−Ligand Recognition

(2010) Riccardo Baron et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Under water's influence

(2010) Gerhard Hummer   Nature Chemistry

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

Computational evaluation of protein–small molecule binding

(2009) Olgun Guvench et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties

(2009) Riccardo Baron et al.   Journal of Chemical Theory and Computation

Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir

(2009) Morgan Lawrenz et al.   Journal of Chemical Theory and Computation

λ-Dynamics free energy simulation methods

(2009) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

(2009) Sarah E. Boyce et al.   JOURNAL OF MOLECULAR BIOLOGY

Prediction of the Water Content in Protein Binding Sites

(2009) Julien Michel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

(2009) Julien Michel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-energy water sites determine peptide binding affinity and specificity of PDZ domains

(2009) Thijs Beuming et al.   PROTEIN SCIENCE

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

(Thermo)dynamic Role of Receptor Flexibility, Entropy, and Motional Correlation in Protein–Ligand Binding

(2008) Riccardo Baron et al.   CHEMPHYSCHEM

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization

(2008) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions

(2008) Clara D. Christ et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

(2008) Mikolai Fajer et al.   Journal of Chemical Theory and Computation

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

(2008) Alan P. Graves et al.   JOURNAL OF MOLECULAR BIOLOGY

The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design

(2008) Tjelvar S.G. Olsson et al.   JOURNAL OF MOLECULAR BIOLOGY

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association

(2008) C.-e. A. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A molecular dynamics approach to study the importance of solvent in protein interactions

(2008) Sergey Samsonov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS