Journal of Computer-Aided Molecular Design

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

G. Madhavi Sastry, Matvey Adzhigirey, Tyler Day et al. · 2013 · 6K citations

Life Sciences, Biochemistry, Bioinformatics +14

Molden: a pre- and post-processing program for molecular and electronic structures*

Gijs Schaftenaar, J. H. Noordik · 2000 · 3.1K citations

Natural Sciences, Chemistry, Materials Science +8

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

Daniel Seeliger, Bert L. de Groot · 2010 · 2.6K citations · Full text

Pharmacy, Bioinformatics, Medicinal Chemistry +14

Epik: a software program for pK a prediction and protonation state generation for drug-like molecules

John C. Shelley, Anuradha Cholleti, Leah L. Frye et al. · 2007 · 2.1K citations

Pharmacy, Medicinal Chemistry, Pharmacology +11

Molecular graph convolutions: moving beyond fingerprints

Steven Kearnes, Kevin McCloskey, Marc Berndl et al. · 2016 · 1.7K citations · Full text

Natural Sciences, Physics, Combinatorial Chemistry +7