Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4

(2014) Arnout R. D. Voet et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of HIV integrase binding from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge

(2014) Alexander L. Perryman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

(2014) Thomas S. Peat et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Allosteric inhibition of HIV-1 integrase activity

(2013) Alan Engelman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process

(2013) Lauren Wickstrom et al.   Journal of Chemical Theory and Computation

Allosteric integrase inhibitor potency is determined through the inhibition of HIV-1 particle maturation

(2013) K. A. Jurado et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perspective: Alchemical free energy calculations for drug discovery

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

Theory of binless multi-state free energy estimation with applications to protein-ligand binding

(2012) Zhiqiang Tan et al.   JOURNAL OF CHEMICAL PHYSICS

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

(2012) Matthew P. Repasky et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)

(2012) Emilio Gallicchio et al.   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

Small Molecule Inhibitors of the LEDGF Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design

(2012) Thomas S. Peat et al.   PLoS One

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

Alchemical free energy methods for drug discovery: progress and challenges

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

Advances in all atom sampling methods for modeling protein–ligand binding affinities

(2011) Emilio Gallicchio et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies

(2011) Anthony K. Felts et al.   Journal of Chemical Information and Modeling

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

(2011) Mauro Lapelosa et al.   Journal of Chemical Theory and Computation

Let’s get honest about sampling

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

Elucidating the Energetics of Entropically Driven Protein–Ligand Association: Calculations of Absolute Binding Free Energy and Entropy

(2011) Nan-jie Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations

(2011) Nan-jie Deng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Virtual screening with AutoDock: theory and practice

(2010) Sandro Cosconati et al.   Expert Opinion on Drug Discovery

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities

(2010) Emilio Gallicchio et al.   Journal of Chemical Theory and Computation

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

(2010) Jeremy R. Greenwood et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A Dynamic Model of HIV Integrase Inhibition and Drug Resistance

(2010) Alex L. Perryman et al.   JOURNAL OF MOLECULAR BIOLOGY

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

The AGBNP2 Implicit Solvation Model

(2009) Emilio Gallicchio et al.   Journal of Chemical Theory and Computation

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Dynamics Study of Non-nucleoside Reverse Transcriptase Inhibitor 4-[[4-[[4-[(E)-2-Cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/Rilpivirine) Aggregates: Correlation between Amphiphilic Properties of the Drug and Oral Bioavailability

(2009) Yulia Volovik Frenkel et al.   JOURNAL OF MEDICINAL CHEMISTRY

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

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

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

In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes

(2008) Mauro Lapelosa et al.   JOURNAL OF MOLECULAR BIOLOGY

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS