CHARMM-GUI 10 years for biomolecular modeling and simulation

Molecular dynamics simulation strategies for protein–micelle complexes

(2016) Xi Cheng et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

(2016) Takaharu Mori et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors

(2016) Evan J. Arthur et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein

(2015) Emilia L. Wu et al.   BIOPHYSICAL JOURNAL

Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes

(2015) Xi Cheng et al.   BIOPHYSICAL JOURNAL

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model

(2015) Yifei Qi et al.   BIOPHYSICAL JOURNAL

Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

(2015) Mingjun Yang et al.   Journal of Chemical Theory and Computation

Conformational Sampling of Oligosaccharides Using Hamiltonian Replica Exchange with Two-Dimensional Dihedral Biasing Potentials and the Weighted Histogram Analysis Method (WHAM)

(2015) Mingjun Yang et al.   Journal of Chemical Theory and Computation

Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy

(2015) Hui Sun Lee et al.   Journal of Chemical Theory and Computation

Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations

(2015) Kira A. Armacost et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

(2015) Yifei Qi et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Membrane Environment Modulates the pKa Values of Transmembrane Helices

(2015) Afra Panahi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulating the Distance Distribution between Spin-Labels Attached to Proteins

(2015) Shahidul M. Islam et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion

(2015) Xiancheng Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

(2015) Jaewoon Jung et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

(2015) Rong Shen et al.   PLoS Computational Biology

CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations

(2014) Yifei Qi et al.   Journal of Chemical Information and Modeling

Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent

(2014) Clément Arnarez et al.   Journal of Chemical Theory and Computation

All-atom polarizable force field for DNA based on the classical drude oscillator model

(2014) Alexey Savelyev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Uncovering pH-Dependent Transient States of Proteins with Buried Ionizable Residues

(2014) Garrett B. Goh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Carbohydrate–Protein Interactions That Drive Processive Polysaccharide Translocation in Enzymes Revealed from a Computational Study of Cellobiohydrolase Processivity

(2014) Brandon C. Knott et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era

(2014) Qiang Cui et al.   PLoS Computational Biology

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

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

Bending Free Energy from Simulation: Correspondence of Planar and Inverse Hexagonal Lipid Phases

(2013) Alexander J. Sodt et al.   BIOPHYSICAL JOURNAL

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics

(2013) Emilia L. Wu et al.   BIOPHYSICAL JOURNAL

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

(2013) Dhruva K. Chakravorty et al.   JOURNAL OF BIOMOLECULAR NMR

CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems

(2013) Xi Cheng et al.   Journal of Chemical Information and Modeling

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

pH-Dependent Dynamics of Complex RNA Macromolecules

(2013) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron–Electron Resonance Spectroscopy

(2013) Benoît Roux et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme

(2013) Shahidul M. Islam et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Chaperone activation by unfolding

(2013) L. Foit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability

(2013) Sean M. Law et al.   PROTEIN SCIENCE

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

(2013) Garrett B. Goh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations

(2012) Adam Hospital et al.   BIOINFORMATICS

Accelerating Membrane Insertion of Peripheral Proteins with a Novel Membrane Mimetic Model

(2012) Y. Zenmei Ohkubo et al.   BIOPHYSICAL JOURNAL

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

(2012) Sunhwan Jo et al.   Journal of Chemical Information and Modeling

Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains

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

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

(2012) Wenbo Yu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Brownian Dynamics Simulations of Ion Transport through the VDAC

(2011) Kyu Il Lee et al.   BIOPHYSICAL JOURNAL

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

(2011) Phillip J. Stansfeld et al.   Journal of Chemical Theory and Computation

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

(2011) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

Multisite λ Dynamics for Simulated Structure–Activity Relationship Studies

(2011) Jennifer L. Knight et al.   Journal of Chemical Theory and Computation

CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling

(2011) Olgun Guvench et al.   Journal of Chemical Theory and Computation

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins

(2011) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores

(2011) Kyu Il Lee et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

MATCH: An atom-typing toolset for molecular mechanics force fields

(2011) Joseph D. Yesselman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

SwissParam: A fast force field generation tool for small organic molecules

(2011) Vincent Zoete et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The future of molecular dynamics simulations in drug discovery

(2011) David W. Borhani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Probing pH-Dependent Dissociation of HdeA Dimers

(2011) Bin W. Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

(2011) Enguerran Vanquelef et al.   NUCLEIC ACIDS RESEARCH

How Fast-Folding Proteins Fold

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

Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids

(2010) Bob Eisenberg et al.   JOURNAL OF CHEMICAL PHYSICS

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

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

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

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function

(2009) Wonpil Im et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL 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

CHARMMing: A New, Flexible Web Portal for CHARMM

(2008) Benjamin T. Miller et al.   Journal of Chemical Information and Modeling

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

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

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

Application of solid-state NMR restraint potentials in membrane protein modeling

(2008) Jinhyuk Lee et al.   JOURNAL OF MAGNETIC RESONANCE

Membrane lipids: where they are and how they behave

(2008) Gerrit van Meer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

(2008) Sunhwan Jo et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Leonardo G. Trabuco et al.   STRUCTURE