Using PyMOL as a platform for computational drug design

Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT1AReceptor

(2016) Shuguang Yuan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Using the PyMOL application to reinforce visual understanding of protein structure

(2016) Rachel E. Rigsby et al.   BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION

Computer Aided Drug Design: Success and Limitations

(2016) Mohammad Hassan Baig et al.   CURRENT PHARMACEUTICAL DESIGN

Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

(2016) Xing Du et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis

(2016) Tomasz Makarewicz et al.   JOURNAL OF MOLECULAR MODELING

A Gating Mechanism of the Serotonin 5-HT 3 Receptor

(2016) Shuguang Yuan et al.   STRUCTURE

Drug design from the cryptic inhibitor envelope

(2016) Chul-Jin Lee et al.   Nature Communications

The Principles of Ligand Specificity on beta-2-adrenergic receptor

(2016) H. C. Stephen Chan et al.   Scientific Reports

The Mechanism of Ligand-Induced Activation or Inhibition of μ- and κ-Opioid Receptors

(2015) Shuguang Yuan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

FlexAID: Revisiting Docking on Non-Native-Complex Structures

(2015) Francis Gaudreault et al.   Journal of Chemical Information and Modeling

LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors

(2015) Samo Lešnik et al.   Journal of Chemical Information and Modeling

PLIP: fully automated protein–ligand interaction profiler

(2015) Sebastian Salentin et al.   NUCLEIC ACIDS RESEARCH

DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit

(2015) Dimitrios Vlachakis et al.   PeerJ

PyTMs: a useful PyMOL plugin for modeling common post-translational modifications

(2014) Andreas Warnecke et al.   BMC BIOINFORMATICS

WATsite: Hydration site prediction program with PyMOL interface

(2014) Bingjie Hu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Combining Structure- and Ligand-Based Approaches to Improve Site of Metabolism Prediction in CYP2C9 Substrates

(2014) Laura J. Kingsley et al.   PHARMACEUTICAL RESEARCH

PharmDock: a pharmacophore-based docking program

(2014) Bingjie Hu et al.   Journal of Cheminformatics

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

(2013) Sander Pronk et al.   BIOINFORMATICS

GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulations

(2013) José Fernando R. Bachega et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite

(2013) Jared Adolf-Bryfogle et al.   PLoS One

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

(2013) David Sehnal et al.   Journal of Cheminformatics

PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

(2012) Emanuele Bramucci et al.   BMC BIOINFORMATICS

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

(2012) Eva Chovancova et al.   PLoS Computational Biology

Mechanisms of Protein-Ligand Association and Its Modulation by Protein Mutations

(2011) Martin Held et al.   BIOPHYSICAL JOURNAL

Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures

(2011) Matthew L. Danielson et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Solvent Interaction Energy Calculations on Molecular Dynamics Trajectories: Increasing the Efficiency Using Systematic Frame Selection

(2011) Markus A. Lill et al.   Journal of Chemical Information and Modeling

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Real-Time PyMOL Visualization for Rosetta and PyRosetta

(2011) Evan H. Baugh et al.   PLoS One

Open Babel: An open chemical toolbox

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

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

(2010) Daniel Seeliger et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Computer-aided drug design platform using PyMOL

(2010) Markus A. Lill et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

LigAlign: Flexible ligand-based active site alignment and analysis

(2010) Abraham Heifets et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

A series of PDB related databases for everyday needs

(2010) R. P. Joosten et al.   NUCLEIC ACIDS RESEARCH