ST-analyzer: A web-based user interface for simulation trajectory analysis

Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

(2013) Saher A. Shaikh et al.   BIOCHEMISTRY

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

(2013) Sander Pronk et al.   BIOINFORMATICS

The Dynamic Process of β2-Adrenergic Receptor Activation

(2013) Rie Nygaard et al.   CELL

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories

(2013) Panagiotis I. Koukos et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain

(2012) Kunal R. Pandit et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Transmembrane Helix Orientation and Dynamics: Insights from Ensemble Dynamics with Solid-State NMR Observables

(2011) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design

(2011) Jacob D. Durrant et al.   Chemical Biology & Drug Design

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Simulation Approaches to Membrane Proteins

(2011) Phillip J. Stansfeld et al.   STRUCTURE

An NMR database for simulations of membrane dynamics

(2010) Avigdor Leftin et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

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

MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

(2010) Tim Meyer et al.   STRUCTURE

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

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Molecular dynamics simulations of membrane channels and transporters

(2009) Fatemeh Khalili-Araghi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Software components for parallel multiscale simulation: an example with LAMMPS

(2009) Benjamin FrantzDale et al.   ENGINEERING WITH COMPUTERS

CHARMM: The biomolecular simulation program

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

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

A conserved protonation-dependent switch controls drug binding in the Abl kinase

(2008) Y. Shan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

(2008) D. A.C. Beck et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data

(2008) C. Kehl et al.   PROTEIN ENGINEERING DESIGN & SELECTION