The Victor C++ library for protein representation and advanced manipulation

Layla Hirsh; Damiano Piovesan; Manuel Giollo; Carlo Ferrari; Silvio C E Tosatto

doi:10.1093/bioinformatics/btu773

The Victor C++ library for protein representation and advanced manipulation

Bioinformatics. 2015 Apr 1;31(7):1138-40. doi: 10.1093/bioinformatics/btu773. Epub 2014 Nov 19.

Authors

Layla Hirsh¹, Damiano Piovesan², Manuel Giollo¹, Carlo Ferrari², Silvio C E Tosatto²

Affiliations

¹ Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy.
² Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, Department of Engineering, Pontificia Universidad Católica del Perú, San Miguel, 32 Lima, Perú and Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy.

PMID: 25414364
DOI: 10.1093/bioinformatics/btu773

Abstract

Motivation: Protein sequence and structure representation and manipulation require dedicated software libraries to support methods of increasing complexity. Here, we describe the VIrtual Constrution TOol for pRoteins (Victor) C++ library, an open source platform dedicated to enabling inexperienced users to develop advanced tools and gathering contributions from the community. The provided application examples cover statistical energy potentials, profile-profile sequence alignments and ab initio loop modeling. Victor was used over the last 15 years in several publications and optimized for efficiency. It is provided as a GitHub repository with source files and unit tests, plus extensive online documentation, including a Wiki with help files and tutorials, examples and Doxygen documentation.

Availability and implementation: The C++ library and online documentation, distributed under a GPL license are available from URL: http://protein.bio.unipd.it/victor/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Databases, Protein*
Humans
Libraries, Digital*
Proteins / chemistry*
Sequence Alignment / methods*
Software*
Structural Homology, Protein

Substances

Proteins