Massimiliano Bonomi1, Carlo Camilloni2,3. 1. Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. 2. Department of Chemistry, Institute for Advanced Study, Technische Universität München, Garching 85747, Germany. 3. Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy.
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.
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.
Authors: Massimiliano Bonomi; Samuel Hanot; Charles H Greenberg; Andrej Sali; Michael Nilges; Michele Vendruscolo; Riccardo Pellarin Journal: Structure Date: 2018-11-01 Impact factor: 5.006
Authors: Erika L Buckle; Arushi Prakash; Massimiliano Bonomi; Janani Sampath; Jim Pfaendtner; Gary P Drobny Journal: J Am Chem Soc Date: 2019-01-24 Impact factor: 15.419
Authors: Mustapha Carab Ahmed; Line K Skaanning; Alexander Jussupow; Estella A Newcombe; Birthe B Kragelund; Carlo Camilloni; Annette E Langkilde; Kresten Lindorff-Larsen Journal: Front Mol Biosci Date: 2021-04-22
Authors: Lisa Eshun-Wilson; Rui Zhang; Didier Portran; Maxence V Nachury; Daniel B Toso; Thomas Löhr; Michele Vendruscolo; Massimiliano Bonomi; James S Fraser; Eva Nogales Journal: Proc Natl Acad Sci U S A Date: 2019-05-09 Impact factor: 11.205