Integrative structural and dynamical biology with PLUMED-ISDB

Abstract

Summary: Accurate structural models of biological systems can be obtained by properly combining experimental data with a priori physico-chemical knowledge. Here we present PLUMED-ISDB, an open-source, freely-available module of the popular PLUMED library, which enables the simultaneous determination of structure and dynamics of conformationally heterogeneous systems by integrating experimental data with a priori information. This integration is achieved using metainference, a general Bayesian framework that accounts for both noise in the data and their ensemble-averaged nature. PLUMED-ISDB implements different types of experimental data, such as several NMR observables, FRET, SAXS and cryo-electron microscopy data, and enables modelling structure and dynamics of individual proteins, protein complexes, membrane proteins, RNA and DNA, using a variety of enhanced sampling methods and resolutions of the system. Availability and implementation: PLUMED-ISDB is freely available at www.plumed.org. Contact: mb2006@cam.ac.uk or carlo.camilloni@unimi.it. Supplementary information: Supplementary data are available at Bioinformatics online.