Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules

(2019) Patrick J. Ropp et al.   Journal of Cheminformatics

BlendMol: advanced macromolecular visualization in Blender

(2018) Jacob D Durrant   BIOINFORMATICS

Design and Development of Highly Potent HIV-1 Protease Inhibitors with a Crown-Like Oxotricyclic Core as the P2-Ligand To Combat Multidrug-Resistant HIV Variants

(2017) Arun K. Ghosh et al.   JOURNAL OF MEDICINAL CHEMISTRY

Scoria: a Python module for manipulating 3D molecular data

(2017) Patrick Ropp et al.   Journal of Cheminformatics

Distributed Drug Discovery: Advancing Chemical Education through Contextualized Combinatorial Solid-Phase Organic Laboratories

(2015) William L. Scott et al.   JOURNAL OF CHEMICAL EDUCATION

Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation

(2015) Sereina Riniker et al.   Journal of Chemical Information and Modeling

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances

(2014) Evanthia Lionta et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

The holistic integration of virtual screening in drug discovery

(2013) Yusuf Tanrikulu et al.   DRUG DISCOVERY TODAY

Structures of human folate receptors reveal biological trafficking states and diversity in folate and antifolate recognition

(2013) A. S. Wibowo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures

(2012) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Parallel distributed computing using Python

(2011) Lisandro D. Dalcin et al.   ADVANCES IN WATER RESOURCES

BINANA: A novel algorithm for ligand-binding characterization

(2011) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Computational ligand-based rational design: role of conformational sampling and force fields in model development

(2011) Jihyun Shim et al.   MedChemComm

Open Babel: An open chemical toolbox

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

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Frog2: Efficient 3D conformation ensemble generator for small compounds

(2010) M. A. Miteva et al.   NUCLEIC ACIDS RESEARCH

Mobyle: a new full web bioinformatics framework

(2009) B. Neron et al.   BIOINFORMATICS

Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery

(2009) J. Santeri Puranen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Distributed Drug Discovery, Part 2: Global Rehearsal of Alkylating Agents for the Synthesis of Resin-Bound Unnatural Amino Acids and Virtual D3Catalog Construction

(2008) William L. Scott et al.   JOURNAL OF COMBINATORIAL CHEMISTRY

Distributed Drug Discovery, Part 1: Linking Academia and Combinatorial Chemistry to Find Drug Leads for Developing World Diseases

(2008) William L. Scott et al.   JOURNAL OF COMBINATORIAL CHEMISTRY

Distributed Drug Discovery, Part 3: Using D3Methodology to Synthesize Analogs of an Anti-Melanoma Compound

(2008) William L. Scott et al.   JOURNAL OF COMBINATORIAL CHEMISTRY

MPI for Python: Performance improvements and MPI-2 extensions

(2007) Lisandro Dalcín et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING