We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural com
mercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-di
mensional SMILES and three-di
mensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical
measure
ments, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experi
ments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at
http://bioware.ucd.ie.