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

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

Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms

(2014) Andrea Cavalli et al.   ACCOUNTS OF CHEMICAL RESEARCH

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

Dual kinase-bromodomain inhibitors for rationally designed polypharmacology

(2014) Pietro Ciceri et al.   Nature Chemical Biology

Targeting bromodomains: epigenetic readers of lysine acetylation

(2014) Panagis Filippakopoulos et al.   NATURE REVIEWS DRUG DISCOVERY

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

(2013) John D. Chodera et al.   Annual Review of Biophysics

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

(2013) Sander Pronk et al.   BIOINFORMATICS

Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields

(2013) Markus K. Dahlgren et al.   Journal of Chemical Information and Modeling

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

Calculating the Sensitivity and Robustness of Binding Free Energy Calculations to Force Field Parameters

(2013) Gabriel J. Rocklin et al.   Journal of Chemical Theory and Computation

Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data

(2013) Lei Huang et al.   Journal of Chemical Theory and Computation

One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery

(2013) Gregory A. Ross et al.   Journal of Chemical Theory and Computation

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

(2013) Kai Wang et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Discovery of Novel Small-Molecule Inhibitors of BRD4 Using Structure-Based Virtual Screening

(2013) Lewis R. Vidler et al.   JOURNAL OF MEDICINAL CHEMISTRY

Optimization of 3,5-Dimethylisoxazole Derivatives as Potent Bromodomain Ligands

(2013) David S. Hewings et al.   JOURNAL OF MEDICINAL CHEMISTRY

Free Energies of Binding from Large-Scale First-Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies

(2013) Stephen J. Fox et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

RVX-208, an inhibitor of BET transcriptional regulators with selectivity for the second bromodomain

(2013) S. Picaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Funnel metadynamics as accurate binding free-energy method

(2013) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

The bromodomain interaction module

(2012) Panagis Filippakopoulos et al.   FEBS LETTERS

Perspective: Alchemical free energy calculations for drug discovery

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

Efficient Algorithms for Langevin and DPD Dynamics

(2012) N. Goga et al.   Journal of Chemical Theory and Computation

Identification of a Chemical Probe for Bromo and Extra C-Terminal Bromodomain Inhibition through Optimization of a Fragment-Derived Hit

(2012) Paul V. Fish et al.   JOURNAL OF MEDICINAL CHEMISTRY

Benzodiazepines and benzotriazepines as protein interaction inhibitors targeting bromodomains of the BET family

(2011) Panagis Filippakopoulos et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Bromodomains as therapeutic targets

(2011) Susanne Muller et al.   EXPERT REVIEWS IN MOLECULAR MEDICINE

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

(2011) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

(2011) Jeff Wereszczynski et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations

(2010) Chunfeng Zhao 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

A Medicinal Chemist’s Guide to Molecular Interactions

(2010) Caterina Bissantz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations

(2009) F. Marty Ytreberg   JOURNAL OF CHEMICAL PHYSICS

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

Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations†

(2009) David L. Mobley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Statistically optimal analysis of samples from multiple equilibrium states

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

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

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

Calculation of protein-ligand binding free energy by using a polarizable potential

(2008) D. Jiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation