NAMD: a Parallel, Object-Oriented Molecular Dynamics Program. - Mark T. Nelson; William Humphrey; Attila Gürsoy; Andrew Dalke; Laxmikant V. Kalé; Robert D. Skeel; Klaus Schulten (Int. J. High Perform. Comput. Appl., 1996)

A Visual Computing Environment for Very Large Scale Biomolecular Modeling. - Michael Zeller; James C. Phillips; Andrew Dalke; William Humphrey; Klaus Schulten; Thomas S. Huang; Vladimir Pavlovic 001; Yunxin Zhao; Zion Lo; Stephen M. Chu; Rajeev Sharma (ASAP, 1997)

Biopython: freely available Python tools for computational molecular biology and bioinformatics. - Peter J. A. Cock; Tiago Rodrigues Antao; Jeffrey T. Chang; Brad A. Chapman; Cymon J. Cox; Andrew Dalke; Iddo Friedberg; Thomas Hamelryck; Frank Kauff; Bartek Wilczynski; Michiel J. L. de Hoon (Bioinform., 2009)

chemfp - fast and portable fingerprint formats and tools. - Andrew Dalke (J. Cheminformatics, 2011)

The FPS fingerprint format and chemfp toolkit. - Andrew Dalke (J. Cheminformatics, 2013)

FMCS: a novel algorithm for the multiple MCS problem. - Andrew Dalke; Janna Hastings (J. Cheminformatics, 2013)

mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets. - Andrew Dalke; Jérôme Hert; Christian Kramer (J. Chem. Inf. Model., 2018)

The chemfp project. - Andrew Dalke (J. Cheminformatics, 2019)

Correction to: The chemfp project. - Andrew Dalke (J. Cheminformatics, 2020)