CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids

We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dime...

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Bibliographic Details
Published in:Journal of chemical information and modeling 2011-04, Vol.51 (4), p.829-836
Main Authors: Duffy, Fergal J, Verniere, Mélanie, Devocelle, Marc, Bernard, Elise, Shields, Denis C, Chubb, Anthony J
Format: Article
Language:English
Subjects:
Algorithms
Amino acids
Amino Acids - chemistry
Analytical chemistry
Applied sciences
Biological and medical sciences
Chemical Information
Chemistry
Computer science
control theory
systems
Computer systems and distributed systems. User interface
Computer-Aided Design
Drug Design
Exact sciences and technology
General and physical chemistry
General pharmacology
General. Nomenclature, chemical documentation, computer chemistry
Internet
Libraries, Digital
Medical sciences
Models, Molecular
Molecular structure
Peptide Library
Peptides
Peptides - chemistry
Peptides, Cyclic - chemistry
Pharmaceutical technology. Pharmaceutical industry
Pharmacology. Drug treatments
Protein synthesis
Software
Theory of reactions, general kinetics. Catalysis. Nomenclature, chemical documentation, computer chemistry
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Summary:We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, 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 experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie.
ISSN:1549-9596
1549-960X
DOI:10.1021/ci100431r