Scalable molecular dynamics on CPU and GPU architectures with NAMD

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

(2020) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism

(2020) Jacob D. Durrant et al.   ACS Central Science

Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field

(2020) Fang-Yu Lin et al.   Journal of Chemical Theory and Computation

Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining

(2019) Jose Antonio Garate et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Analysis of the adaptive multilevel splitting method on the isomerization of alanine dipeptide

(2019) Laura J. S. Lopes et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Addressing Polarization Phenomena in Molecular Machines Containing Transition Metal Ions with an Additive Force Field

(2019) Shuangli Du et al.   Journal of Chemical Theory and Computation

Accelerating Membrane Simulations with Hydrogen Mass Repartitioning

(2019) Curtis Balusek et al.   Journal of Chemical Theory and Computation

pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase

(2019) Ankita Sarkar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution

(2019) Yixin Cen et al.   Nature Communications

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD

(2019) Wei Jiang et al.   Journal of Chemical Information and Modeling

Taming Rugged Free Energy Landscapes Using an Average Force

(2019) Haohao Fu et al.   ACCOUNTS OF CHEMICAL RESEARCH

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

(2019) Abhishek Singharoy et al.   CELL

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

(2019) Giacomo Fiorin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

QM/MM methods for free energies and photochemistry

(2018) Eliot Boulanger et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations

(2018) Haohao Fu et al.   Journal of Chemical Information and Modeling

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator

(2018) Donghyuk Suh et al.   JOURNAL OF CHEMICAL PHYSICS

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation

(2018) Yu-ming M. Huang et al.   Journal of Chemical Theory and Computation

Link between Membrane Composition and Permeability to Drugs

(2018) Chi Hang Tse et al.   Journal of Chemical Theory and Computation

NAMD goes quantum: an integrative suite for hybrid simulations

(2018) Marcelo C R Melo et al.   NATURE METHODS

Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding

(2018) Leah V. Sibener et al.   CELL

Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys

(2018) Haohao Fu et al.   Journal of Physical Chemistry Letters

A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol

(2018) Reza Salari et al.   Journal of Chemical Theory and Computation

Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements

(2018) Fabrizio Marinelli et al.   STRUCTURE

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies

(2017) Haohao Fu et al.   Journal of Chemical Theory and Computation

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

(2017) Brian K. Radak et al.   Journal of Chemical Theory and Computation

Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase

(2017) Robert C. Harris et al.   Journal of Physical Chemistry Letters

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost

(2017) J. S. Smith et al.   Chemical Science

Software update: the ORCA program system, version 4.0

(2017) Frank Neese   Wiley Interdisciplinary Reviews-Computational Molecular Science

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

(2016) Justin A. Lemkul et al.   CHEMICAL REVIEWS

Power, Reliability, and Performance: One System to Rule them All

(2016) Bilge Acun et al.   COMPUTER

Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

(2016) Brian K. Radak et al.   JOURNAL OF CHEMICAL PHYSICS

Gaussian Accelerated Molecular Dynamics in NAMD

(2016) Yui Tik Pang et al.   Journal of Chemical Theory and Computation

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations

(2016) Haohao Fu et al.   Journal of Chemical Theory and Computation

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water

(2016) Yandong Huang 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

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

(2016) Garima Jindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method

(2016) Adrien Lesage et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors

(2016) Christopher R. Ellis et al.   Journal of Physical Chemistry Letters

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2

(2016) Abhishek Singharoy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Advances in the molecular dynamics flexible fitting method for cryo-EM modeling

(2016) Ryan McGreevy et al.   METHODS

An alternative construction of the Ewald sum

(2016) Robert D. Skeel   MOLECULAR PHYSICS

Mechanical Trapping of DNA in a Double-Nanopore System

(2016) Sergii Pud et al.   NANO LETTERS

Subdiffusion in Membrane Permeation of Small Molecules

(2016) Christophe Chipot et al.   Scientific Reports

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

(2016) Sérgio Filipe Sousa et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

(2016) Abhishek Singharoy et al.   eLife

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

(2016) João V. Ribeiro et al.   Scientific Reports

Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA

(2015) Maxim Belkin et al.   ACS Nano

Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations

(2015) Thakshila Dissanayake et al.   BIOCHEMISTRY

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics

(2015) Urmi Doshi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions

(2015) Fabrizio Marinelli et al.   BIOPHYSICAL JOURNAL

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

(2015) Matthew G. Quesne et al.   CHEMISTRY-A EUROPEAN JOURNAL

Molecular dynamics simulations of large macromolecular complexes

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

Using Migratable Objects to Enhance Fault Tolerance Schemes in Supercomputers

(2015) Esteban Meneses et al.   IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS

Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics—Monte Carlo simulations

(2015) Yunjie Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Multilevel Summation Method for Electrostatic Force Evaluation

(2015) David J. Hardy et al.   Journal of Chemical Theory and Computation

Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

(2015) Yunjie Chen et al.   Journal of Chemical Theory and Computation

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

(2015) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles

(2015) Abhishek Singharoy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis

(2015) Boon Chong Goh et al.   STRUCTURE

Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter

(2015) Mary Hongying Cheng et al.   STRUCTURE

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments

(2015) Rong Shen et al.   PLoS Computational Biology

Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

(2014) Yunjie Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data

(2014) Andrew D. White et al.   Journal of Chemical Theory and Computation

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules

(2014) Jeffrey Comer et al.   Journal of Chemical Theory and Computation

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

(2014) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

(2014) Juyong Lee et al.   Journal of Chemical Theory and Computation

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

(2014) Jason M. Swails et al.   Journal of Chemical Theory and Computation

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

(2014) Jeffrey Comer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain

(2014) Qufei Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I

(2014) V. R. I. Kaila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling thermophoretic effects in solid-state nanopores

(2014) Maxim Belkin et al.   Journal of Computational Electronics

Predicting enzymatic reactivity: from theory to design

(2014) Katarzyna Świderek et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin

(2014) Thomas R. Caulfield et al.   PLoS Computational Biology

A structural model of the active ribosome-bound membrane protein insertase YidC

(2014) Stephan Wickles et al.   eLife

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

(2014) Ryan McGreevy et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores

(2013) Maxim Belkin et al.   ACS Nano

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD

(2013) Wei Jiang et al.   COMPUTER PHYSICS COMMUNICATIONS

Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations

(2013) Jeffrey Comer et al.   Journal of Chemical Theory and Computation

Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations

(2013) Bogdan Lev et al.   Journal of Chemical Theory and Computation

Using collective variables to drive molecular dynamics simulations

(2013) Giacomo Fiorin et al.   MOLECULAR PHYSICS

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

The description of electronic processes inside proteins from Car-Parrinello molecular dynamics: chemical transformations

(2013) Carme Rovira   Wiley Interdisciplinary Reviews-Computational Molecular Science

Frontiers in free-energy calculations of biological systems

(2013) Christophe Chipot   Wiley Interdisciplinary Reviews-Computational Molecular Science

Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction

(2012) Rafael C. Bernardi et al.   Journal of Chemical Theory and Computation

Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer

(2012) Wei Jiang et al.   Journal of Chemical Theory and Computation

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

On the Use of Experimental Observations to Bias Simulated Ensembles

(2012) Jed W. Pitera et al.   Journal of Chemical Theory and Computation

GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations

(2012) Julio Daniel Carvalho Maia et al.   Journal of Chemical Theory and Computation

GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations

(2012) David E. Tanner et al.   Journal of Chemical Theory and Computation

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

(2012) James J. P. Stewart   JOURNAL OF MOLECULAR MODELING

Path Finding on High-Dimensional Free Energy Landscapes

(2012) Grisell Díaz Leines et al.   PHYSICAL REVIEW LETTERS

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

(2012) J. Wereszczynski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein

(2011) Denis Bucher et al.   BIOCHEMISTRY

Stereochemical errors and their implications for molecular dynamics simulations

(2011) Eduard Schreiner et al.   BMC BIOINFORMATICS

Alchemical free energy methods for drug discovery: progress and challenges

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

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

(2011) Serena Donnini et al.   Journal of Chemical Theory and Computation

Parallel Generalized Born Implicit Solvent Calculations with NAMD

(2011) David E. Tanner et al.   Journal of Chemical Theory and Computation

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

(2011) Jason A. Wallace et al.   Journal of Chemical Theory and Computation

Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

(2011) Yi Wang 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

Cryo-EM structure of the ribosome–SecYE complex in the membrane environment

(2011) Jens Frauenfeld et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Enhanced Sampling of Multidimensional Free-Energy Landscapes Using Adaptive Biasing Forces

(2011) Christophe Chipot et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Symmetry-Restrained Flexible Fitting for Symmetric EM Maps

(2011) Kwok-Yan Chan et al.   STRUCTURE

The empirical valence bond model: theory and applications

(2011) Shina C. L. Kamerlin et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The ORCA program system

(2011) Frank Neese   Wiley Interdisciplinary Reviews-Computational Molecular Science

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation

(2010) David B. Wells et al.   BIOPHYSICAL JOURNAL

OpenMM: A Hardware-Independent Framework for Molecular Simulations

(2010) Peter Eastman et al.   COMPUTING IN SCIENCE & ENGINEERING

Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system

(2010) S. Kumar et al.   IBM JOURNAL OF RESEARCH AND DEVELOPMENT

Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach

(2010) K. Minoukadeh et al.   Journal of Chemical Theory and Computation

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

(2010) Wei Jiang et al.   Journal of Chemical Theory and Computation

Carboxyl pKa Values and Acid Denaturation of BBL

(2010) Eyal Arbely et al.   JOURNAL OF MOLECULAR BIOLOGY

GPU-accelerated molecular modeling coming of age

(2010) John E. Stone et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

(2010) Wei Jiang et al.   Journal of Physical Chemistry Letters

Applications of the molecular dynamics flexible fitting method

(2010) Leonardo G. Trabuco et al.   JOURNAL OF STRUCTURAL BIOLOGY

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

(2009) Jérome Hénin et al.   Journal of Chemical Theory and Computation

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography

(2009) Leonardo G. Trabuco et al.   METHODS

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

(2009) E. Villa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Exchange frequency in replica exchange molecular dynamics

(2008) Daniel Sindhikara et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Downhill versus Barrier-Limited Folding of BBL 1: Energetic and Structural Perturbation Effects upon Protonation of a Histidine of Unusually Low pKa

(2008) Eyal Arbely et al.   JOURNAL OF MOLECULAR BIOLOGY

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE