Binding free energy calculations on E-selectin complexes with sLex oligosaccharide analogs

Accurate calculation of the absolute free energy of binding for drug molecules

(2016) Matteo Aldeghi et al.   Chemical Science

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Protein-Carbohydrate Interactions Studied by NMR: From Molecular Recognition to Drug Design

(2013) Maria del Carmen Fernandez-Alonso et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

A Comparative Molecular Dynamics, MM–PBSA and Thermodynamic Integration Study of Saquinavir Complexes with Wild-Type HIV-1 PR and L10I, G48V, L63P, A71V, G73S, V82A and I84V Single Mutants

(2013) Haralambos Tzoupis et al.   Journal of Chemical Theory and Computation

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI

(2013) Sílvia A. Martins et al.   Journal of Chemical Theory and Computation

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Sialyl Lewisx: A “Pre-Organized Water Oligomer”?

(2012) Florian P. C. Binder et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations

(2012) Mehrnoosh Arrar et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Characterization of Domain–Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein–Protein Interaction Network in Yeast by Generic Structure-Based Models

(2012) Tingjun Hou et al.   JOURNAL OF PROTEOME RESEARCH

Predicting the Effects of Basepair Mutations in DNA-Protein Complexes by Thermodynamic Integration

(2011) Frank R. Beierlein et al.   BIOPHYSICAL JOURNAL

Pre-organization of the Core Structure of E-Selectin Antagonists

(2011) Daniel Schwizer et al.   CHEMISTRY-A EUROPEAN JOURNAL

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

(2011) Samuel Genheden et al.   Journal of Chemical Information and Modeling

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

(2011) Thomas Steinbrecher et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan–protein complexes

(2010) Robert J Woods et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Limits of Free Energy Computation for Protein−Ligand Interactions

(2010) Kenneth M. Merz   Journal of Chemical Theory and Computation

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Statistically optimal analysis of samples from multiple equilibrium states

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