Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

Protein Flexibility and Ligand Recognition: Challenges for Molecular Modeling

(2012) Francesca Spyrakis et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Ligand-Steered Modeling and Docking: A Benchmarking Study in Class A G-Protein-Coupled Receptors

(2010) Sharangdhar S. Phatak et al.   Journal of Chemical Information and Modeling

Modeling Protein−Ligand Binding by Mining Minima

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

Docking-based virtual screening for ligands of G protein-coupled receptors: Not only crystal structures but also in silico models

(2010) Santiago Vilar et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

(2010) Jindřich Fanfrlík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Quantum Mechanical Dynamics of Charge Transfer in Ubiquitin in Aqueous Solution

(2009) Victor M. Anisimov et al.   CHEMPHYSCHEM

Study of MDM2 Binding to p53-Analogues: Affinity, Helicity, and Applicability to Drug Design

(2009) Ori Kalid et al.   Journal of Chemical Information and Modeling

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water

(2009) Wangshen Xie et al.   Journal of Chemical Theory and Computation

Performance of the IEF-MST Solvation Continuum Model in a Blind Test Prediction of Hydration Free Energies†

(2009) Ignacio Soteras et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculation of Protein−Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects

(2009) Pär Söderhjelm et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Binding Mode of Petrosaspongiolide M to the Human Group IIA Phospholipase A2: Exploring the Role of Covalent and Noncovalent Interactions in the Inhibition Process

(2008) Maria Chiara Monti et al.   CHEMISTRY-A EUROPEAN JOURNAL

Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility

(2008) Claudio Cavasotto et al.   Current Computer-Aided Drug Design

Assessment of programs for ligand binding affinity prediction

(2008) Ryangguk Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Toward accurate relative energy predictions of the bioactive conformation of drugs

(2008) Keith T. Butler et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Is Quantum Mechanics Necessary for Predicting Binding Free Energy?

(2008) Ting Zhou et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

(2008) Qizhi Cui et al.   JOURNAL OF MOLECULAR BIOLOGY

Application of the PM6 method to modeling proteins

(2008) James J. P. Stewart   JOURNAL OF MOLECULAR MODELING

Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases

(2008) Ileana Stoica et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Binding specificity of SH2 domains: Insight from free energy simulations

(2008) Wenxun Gan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS