Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

Assessment of Binding Affinity via Alchemical Free Energy Calculations

(2020) Maximilian Kuhn et al.   Journal of Chemical Information and Modeling

Insights from Earth system model initial-condition large ensembles and future prospects

(2020) C. Deser et al.   Nature Climate Change

Principles Governing Control of Aggregation and Dispersion of Graphene and Graphene Oxide in Polymer Melts

(2020) James L. Suter et al.   ADVANCED MATERIALS

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

(2020) Christina E. M. Schindler et al.   Journal of Chemical Information and Modeling

Large-scale binding affinity calculations on commodity compute clouds

(2020) S. J. Zasada et al.   Interface Focus

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

(2020) Shunzhou Wan et al.   Interface Focus

Chemical Crystallography: when are ‘ bad data’ ‘good data’?

(2019) Amber L. Thompson   Crystallography Reviews

Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning

(2019) Raquel Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A2A Receptor Binders

(2019) Andrew Potterton et al.   Journal of Chemical Theory and Computation

Predicting Activity Cliffs with Free-Energy Perturbation

(2019) Laura Pérez-Benito et al.   Journal of Chemical Theory and Computation

Molecular simulation of peptides coming of age: Accurate prediction of folding, dynamics and structures

(2019) Panagiota S. Georgoulia et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Kinetics of Drug Binding and Residence Time

(2019) Mattia Bernetti et al.   Annual Review of Physical Chemistry

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

(2019) David W. Wright et al.   Scientific Reports

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

(2019) Vytautas Gapsys et al.   eLife

Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

(2019) Krystel El Hage et al.   eLife

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches

(2019) Matteo Aldeghi et al.   ACS Central Science

Preface for focus issue on uncertainty quantification in materials modeling

(2019) Stephen Foiles et al.   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes

(2018) Jakob P. Ulmschneider et al.   ACCOUNTS OF CHEMICAL RESEARCH

HPC Cloud for Scientific and Business Applications

(2018) Marco A. S. Netto et al.   ACM COMPUTING SURVEYS

Graphene-Graphene Interactions: Friction, Superlubricity, and Exfoliation

(2018) Robert C. Sinclair et al.   ADVANCED MATERIALS

Ensemble Docking in Drug Discovery

(2018) Rommie E. Amaro et al.   BIOPHYSICAL JOURNAL

Simulations meet machine learning in structural biology

(2018) Adrià Pérez et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The rise of deep learning in drug discovery

(2018) Hongming Chen et al.   DRUG DISCOVERY TODAY

Distributed data-driven platform for urgent decision making in cardiological ambulance control

(2018) Sergey V. Kovalchuk et al.   Future Generation Computer Systems-The International Journal of eScience

Holistic approach to management of IT infrastructure for environmental monitoring and decision support systems with urgent computing capabilities

(2018) Bartosz Balis et al.   Future Generation Computer Systems-The International Journal of eScience

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

(2018) Daria B. Kokh et al.   Journal of Chemical Theory and Computation

Uncertainty Quantification in Alchemical Free Energy Methods

(2018) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Assessing the stability of free-energy perturbation calculations by performing variations in the method

(2018) Francesco Manzoni et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

(2018) Krystel El Hage et al.   eLife

Reproducibility vs. Replicability: A Brief History of a Confused Terminology

(2018) Hans E. Plesser   Frontiers in Neuroinformatics

The ECMWF Ensemble Prediction System: Looking Back (more than) 25 Years and Projecting Forward 25 Years

(2018) T.N. Palmer   QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY

High-throughput binding affinity calculations at extreme scales

(2018) Jumana Dakka et al.   BMC BIOINFORMATICS

Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges

(2018) Wei Chen et al.   Journal of Chemical Theory and Computation

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages

(2018) Hannes H. Loeffler et al.   Journal of Chemical Theory and Computation

Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas

(2018) Bernhard Knapp et al.   Journal of Chemical Theory and Computation

Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding

(2018) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation

(2017) Shunzhou Wan et al.   Journal of Chemical Information and Modeling

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study

(2017) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

An Ensemble-Based Protocol for the Computational Prediction of Helix–Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics

(2017) Nojood A. Altwaijry et al.   Journal of Chemical Theory and Computation

Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry

(2017) Billy J. Williams-Noonan et al.   JOURNAL OF MEDICINAL CHEMISTRY

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Water, water, everywhere… It's time to stop and think

(2016) Michael S. Bodnarchuk   DRUG DISCOVERY TODAY

The Deluge of Spurious Correlations in Big Data

(2016) Cristian S. Calude et al.   Foundations of Science

Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration

(2016) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time

(2016) Ivan Teo et al.   Journal of Chemical Theory and Computation

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

(2016) Bradley Sherborne et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Innovation in the pharmaceutical industry: New estimates of R&D costs

(2016) Joseph A. DiMasi et al.   JOURNAL OF HEALTH ECONOMICS

1,500 scientists lift the lid on reproducibility

(2016) Monya Baker   NATURE

On the calculation of equilibrium thermodynamic properties from molecular dynamics

(2016) Peter V. Coveney et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2016) Matteo Aldeghi et al.   Chemical Science

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

FESetup: Automating Setup for Alchemical Free Energy Simulations

(2015) Hannes H. Loeffler et al.   Journal of Chemical Information and Modeling

Accurate Binding Free Energy Predictions in Fragment Optimization

(2015) Thomas B. Steinbrecher et al.   Journal of Chemical Information and Modeling

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

(2015) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

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

The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study

(2015) Tom D. Bunney et al.   EBioMedicine

Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

(2014) Pedro J. Ballester 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

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

(2014) Yen-Lin Lin et al.   Journal of Chemical Theory and Computation

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

(2014) Nadine Homeyer et al.   Journal of Chemical Theory and Computation

pmx: Automated protein structure and topology generation for alchemical perturbations

(2014) Vytautas Gapsys et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations

(2014) Magnus Lundborg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

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

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

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Improved Ligand Binding Energies Derived from Molecular Dynamics: Replicate Sampling Enhances the Search of Conformational Space

(2013) Marc Adler et al.   Journal of Chemical Information and Modeling

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

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

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

Lead optimization mapper: automating free energy calculations for lead optimization

(2013) Shuai Liu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Mechanism of Drug Efficacy Within the EGF Receptor Revealed by Microsecond Molecular Dynamics Simulation

(2012) S. Wan et al.   MOLECULAR CANCER THERAPEUTICS

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen 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

From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine

(2012) David W. Wright et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods

(2011) Himanshu Paliwal et al.   Journal of Chemical Theory and Computation

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs

(2011) S. Wan et al.   Journal of the Royal Society Interface

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

Reproducible Research in Computational Science

(2011) R. D. Peng   SCIENCE

Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes

(2010) Eva Stjernschantz et al.   BIOPHYSICAL JOURNAL

Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases

(2010) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

(2010) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Determination of Free Energy Profiles for the Translocation of Polynucleotides through α-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations

(2009) Hugh S. C. Martin et al.   Journal of Chemical Theory and Computation

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir

(2009) Morgan Lawrenz et al.   Journal of Chemical Theory and Computation

Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics

(2009) Wei Jiang et al.   Journal of Chemical Theory and Computation

Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases

(2008) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

Statistically optimal analysis of samples from multiple equilibrium states

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

Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase

(2008) Lily S. Cheng et al.   JOURNAL OF MEDICINAL CHEMISTRY

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

(2007) N Moitessier et al.   BRITISH JOURNAL OF PHARMACOLOGY