Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations

(2020) Hugo Guterres et al.   Journal of Chemical Information and Modeling

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)

(2019) Tharindu Senapathi et al.   BIOINFORMATICS

NGL viewer: web-based molecular graphics for large complexes

(2018) Alexander S Rose et al.   BIOINFORMATICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Community-Driven Data Analysis Training for Biology

(2018) Bérénice Batut et al.   Cell Systems

Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics

(2018) Doris A. Schuetz et al.   Journal of Chemical Information and Modeling

Escaping Atom Types in Force Fields Using Direct Chemical Perception

(2018) David L. Mobley et al.   Journal of Chemical Theory and Computation

The HSP90 chaperone machinery

(2017) Florian H. Schopf et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Water models for biomolecular simulations

(2017) Alexey V. Onufriev et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Integrating protein structural dynamics and evolutionary analysis with Bio3D

(2014) Lars Skjærven et al.   BMC BIOINFORMATICS

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

(2014) Sergio Ruiz-Carmona et al.   PLoS Computational Biology

BioBlend: automating pipeline analyses within Galaxy and CloudMan

(2013) C. Sloggett et al.   BIOINFORMATICS

High-throughput molecular dynamics: the powerful new tool for drug discovery

(2012) Matthew J. Harvey et al.   DRUG DISCOVERY TODAY

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

(2012) Maria M. Reif et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

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

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors

(2010) Antonija Kuzmanic et al.   BIOPHYSICAL JOURNAL

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY