Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables

• DOI: 10.1093/bioinformatics/bts172
• Publication Date: 2012-05-21T06:03:24Z
• Authors: Valéry Ozenne; Frédéric Bauer; Loïc Salmon; Jie-rong Huang; Malene Ringkjøbin...; Stéphane Segard; Pau Bernadó; Céline Charavay; Martin Blackledge
• Keywords: Intrinsically Disordered Proteins; Conformational ensembles; Conformational isomerism; Executable

Abstract Motivation: Intrinsically disordered proteins (IDPs) represent a significant fraction of the human proteome. The classical structure function paradigm that has successfully underpinned our understanding molecular biology breaks down when considering have no stable tertiary in their functional form. One convenient approach is to describe protein terms an equilibrium rapidly inter-converting conformers. Currently, tools generate such ensemble descriptions are extremely rare, and poorly adapted prediction experimental data. Results: We present flexible-meccano—a highly efficient algorithm generates ensembles molecules, on basis amino acid-specific conformational potentials volume exclusion. Conformational sampling depends uniquely primary sequence, with possibility introducing additional local or long-range propensities at resolution. can also be used calculate expected values parameters measured atomic resolution, as nuclear magnetic resonance (NMR) small angle scattering, respectively. envisage flexible-meccano will useful for researchers who wish compare data those from fully protein, see evidence deviation ‘random coil’ behaviour interested working broad conformers representing flexibility IDP interest. Availability: A documented multi-platform executable provided, examples, http://www.ibs.fr/science-213/scientific-output/software/flexible-meccano/ Contact: [e-mail]