22 / 161
Conformational Ensembles from Experimental Data
and Computer Simulations
Sunday Speaker Abstracts
18
Integrative Structural and Dynamical Biology with PLUMED-ISDB
Massimiliano Bonomi
1
, Carlo Camilloni
2
, Michele Vendruscolo
1
.
1
University of Cambridge, Cambridge, United Kingdom,
2
Technische Universität München,
Garching, Germany.
Accurate structural models of biological systems can be obtained by properly combining
multiple sources of information, such as experimental data and a priori physico-chemical
knowledge [1]. Here we present PLUMED-ISDB, an open-source, freely-available module of the
popular PLUMED library
[www.plumed.org; 2], 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 [3],
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 [4], 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.
[1] M. Bonomi, G. T. Heller, C. Camilloni, M. Vendruscolo, Principles of protein structural
ensemble determination. Curr. Opin. Struct. Biol. 42, 106-116 (2017).
[2] G. A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, PLUMED 2: New
feathers for an old bird. Comp. Phys. Comm. 185, 604-613 (2014).
[3] M. Bonomi, C. Camilloni, A. Cavalli, M. Vendruscolo, Metainference: A Bayesian inference
method for heterogeneous systems. Sci. Adv. 2, e1501177 (2016).
[4] S. Hanot et al., Multi-scale Bayesian modelling of cryo-electron microscopy density maps.
bioRxiv doi: 10.1101/113951 (2017).