Binding free energy, energy and entropy calculations using simple model systems

SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors

(2012) A. Geoffrey Skillman   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

(2012) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation

(2011) Nathan Schmid et al.   COMPUTER PHYSICS COMMUNICATIONS

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Biophysical and physicochemical methods differentiate highly ligand-efficient human D-amino acid oxidase inhibitors

(2011) Jos H.M. Lange et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters

(2011) Bruno A. C. Horta et al.   Journal of Chemical Theory and Computation

Calculation of Configurational Entropy with a Boltzmann–Quasiharmonic Model: The Origin of High-Affinity Protein–Ligand Binding

(2011) Kyle W. Harpole et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software

(2011) Sereina Riniker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Survey of the year 2009: applications of isothermal titration calorimetry

(2010) Robert J. Falconer et al.   JOURNAL OF MOLECULAR RECOGNITION

Water in Cavity−Ligand Recognition

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

Estimating Absolute Configurational Entropies of Macromolecules: The Minimally Coupled Subspace Approach

(2010) Ulf Hensen et al.   PLoS One

A Thermodynamic Approach to the Affinity Optimization of Drug Candidates

(2009) Ernesto Freire   Chemical Biology & Drug Design

Absolute Hydration Entropies of Alkali Metal Ions from Molecular Dynamics Simulations

(2009) Jens Carlsson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thermodynamic and Structural Effects of Conformational Constraints in Protein−Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization

(2009) John E. DeLorbe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Adding calorimetric data to decision making in lead discovery: a hot tip

(2009) John E. Ladbury et al.   NATURE REVIEWS DRUG DISCOVERY

Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces

(2009) Ulf Hensen et al.   PHYSICAL REVIEW E

Do enthalpy and entropy distinguish first in class from best in class?

(2008) E FREIRE   DRUG DISCOVERY TODAY

Efficient free energy calculations on small molecule host-guest systems-A combined linear interaction energy/one-step perturbation approach

(2008) Chris Oostenbrink   JOURNAL OF COMPUTATIONAL CHEMISTRY