Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation

Uncertainty quantification in classical molecular dynamics

(2021) Shunzhou Wan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Reliability and reproducibility in computational science: implementing validation, verification and uncertainty quantification in silico

(2021) Peter V. Coveney et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations

(2021) D. Groen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Building Confidence in Simulation: Applications of EasyVVUQ

(2020) David W. Wright et al.   Advanced Theory and Simulations

Computational biomedicine. Part 1: molecular medicine

(2020) Peter V. Coveney   Interface Focus

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

(2020) Shunzhou Wan et al.   Interface Focus

On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

(2020) Vytautas Gapsys et al.   eLife

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

(2020) Lorenzo Casalino et al.   ACS Central Science

Big data: the end of the scientific method?

(2019) Sauro Succi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

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

Adaptive multi‐index collocation for uncertainty quantification and sensitivity analysis

(2019) John D. Jakeman et al.   INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

(2018) Xiu Yang et al.   Journal of Chemical Theory and Computation

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

(2018) Krystel El Hage et al.   eLife

Deep UQ: Learning deep neural network surrogate models for high dimensional uncertainty quantification

(2018) Rohit K. Tripathy et al.   JOURNAL OF COMPUTATIONAL PHYSICS

High-throughput binding affinity calculations at extreme scales

(2018) Jumana Dakka et al.   BMC BIOINFORMATICS

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

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

Overview of the SAMPL6 host–guest binding affinity prediction challenge

(2018) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

(2016) Caitlin C. Bannan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Big data need big theory too

(2016) Peter V. Coveney et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

On the calculation of equilibrium thermodynamic properties from molecular dynamics

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

Chaospy: An open source tool for designing methods of uncertainty quantification

(2015) Jonathan Feinberg et al.   Journal of Computational Science

Blind prediction of solvation free energies from the SAMPL4 challenge

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

The Discovery of I-BET726 (GSK1324726A), a Potent Tetrahydroquinoline ApoA1 Up-Regulator and Selective BET Bromodomain Inhibitor

(2014) Romain Gosmini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Adaptive Leja Sparse Grid Constructions for Stochastic Collocation and High-Dimensional Approximation

(2014) Akil Narayan et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Bayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing framework

(2012) Panagiotis Angelikopoulos et al.   JOURNAL OF CHEMICAL PHYSICS

Uncertainty Quantification in MD Simulations. Part II: Bayesian Inference of Force-Field Parameters

(2012) F. Rizzi et al.   MULTISCALE MODELING & SIMULATION

Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations

(2011) David W. Wright et al.   Journal of Chemical Information and Modeling

Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

(2011) Samuel Genheden et al.   Journal of Chemical Theory and Computation