Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

Postprocessing of Docked Protein−Ligand Complexes Using Implicit Solvation Models

(2011) Anton Lindström et al.   Journal of Chemical Information and Modeling

Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions

(2011) Allyn R. Brice et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Virtual screening using molecular simulations

(2011) Tianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

(2011) Yu-ming M Huang et al.   BMC Biophysics

Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity

(2011) Daniel J. Cole et al.   PLoS Computational Biology

Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin

(2011) Ioan Iacovache et al.   PLoS Pathogens

Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity

(2010) C. Wichmann et al.   BLOOD

Role of Water Molecules in Structure and Energetics ofPseudomonas aeruginosaLectin I Interacting with Disaccharides

(2010) Alessandra Nurisso et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5′-UAA/5′-GAN Internal Loops Studied by Molecular Dynamics Methods

(2010) Kamila Réblová et al.   Journal of Chemical Theory and Computation

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cooperativity and Specificity of Cys2His2Zinc Finger Protein−DNA Interactions: A Molecular Dynamics Simulation Study

(2010) Juyong Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rigorous Free Energy Calculations in Structure-Based Drug Design

(2010) Julien Michel  et al.   Molecular Informatics

Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides

(2010) Neil J. Bruce et al.   PEPTIDES

Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction

(2010) Richard T. Bradshaw et al.   PROTEIN ENGINEERING DESIGN & SELECTION

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

How accurate are continuum solvation models for drug-like molecules?

(2009) Jacob Kongsted et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The crystal structure of the AF2331 protein fromArchaeoglobus fulgidusDSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold

(2009) Shuren Wang et al.   PROTEIN SCIENCE

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

(2009) Noriaki Okimoto et al.   PLoS Computational Biology

Computational analysis of the binding affinities of the natural-product cyclopentapeptides argifin and argadin to chitinase B from Serratia marcescens

(2008) Hiroaki Gouda et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Investigation of MM-PBSA Rescoring of Docking Poses

(2008) David C. Thompson et al.   Journal of Chemical Information and Modeling

An improved method to predict the entropy term with the MM/PBSA approach

(2008) Jacob Kongsted et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure and folding of disulfide-rich miniproteins: Insights from molecular dynamics simulations and MM-PBSA free energy calculations

(2008) Cecil Combelles et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS