Lead optimization mapper: automating free energy calculations for lead optimization

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

(2013) Lingle Wang et al.   Journal of Chemical Theory and Computation

FEW: A workflow tool for free energy calculations of ligand binding

(2013) Nadine Homeyer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Perspective: Alchemical free energy calculations for drug discovery

(2012) David L. Mobley et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors

(2012) Anita de Ruiter et al.   Journal of Chemical Theory and Computation

Computation of the binding affinities of catechol-O-methyltransferase inhibitors: Multisubstate relative free energy calculations

(2012) P. Nuno Palma et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

(2012) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arylsulfonamidopiperidone derivatives as a novel class of factor Xa inhibitors

(2011) Yan Shi et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Structure and property based design of factor Xa inhibitors: Pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs

(2011) Robert J. Young et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Avoiding the van der Waals endpoint problem using serial atomic insertion

(2011) Stefan Boresch et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The DINGO dataset: a comprehensive set of data for the SAMPL challenge

(2011) Janet Newman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Alchemical prediction of hydration free energies for SAMPL

(2011) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies

(2010) Thomas Steinbrecher et al.   CURRENT MEDICINAL CHEMISTRY

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

(2010) James Luccarelli et al.   Journal of Chemical Theory and Computation

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

(2010) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Design, synthesis, and SAR of cis-1,2-diaminocyclohexane derivatives as potent factor Xa inhibitors. Part II: Exploration of 6–6 fused rings as alternative S1 moieties

(2009) Kenji Yoshikawa et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Design, synthesis, and SAR of cis-1,2-diaminocyclohexane derivatives as potent factor Xa inhibitors. Part I: Exploration of 5–6 fused rings as alternative S1 moieties

(2009) Kenji Yoshikawa et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

(2009) David L. Mobley et al.   Journal of Chemical Theory and Computation

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

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Can we use docking and scoring for hit-to-lead optimization?

(2008) Istvan J. Enyedy et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules

(2008) David L. Mobley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Strategies and tactics for optimizing the Hit-to-Lead process and beyond—A computational chemistry perspective

(2007) C MANLY et al.   DRUG DISCOVERY TODAY