Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well as with system heterogeneity. Furthermore, metainference can be implemented using the metadynamics approach, which enables the computational study of complex biological systems requiring extensive conformational sampling. In this chapter, we provide a step-by-step guide to perform and analyse metadynamic metainference simulations using the ISDB module of the open-source PLUMED library, as well as a series of practical tips to avoid common mistakes. Specifically, we will guide the reader in the process of learning how to model the structural ensemble of a small disordered peptide by combining state-of-the-art molecular mechanics force fields with nuclear magnetic resonance data, including chemical shifts, scalar couplings and residual dipolar couplings.

A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference / T. Löhr, C. Camilloni, M. Bonomi, M. Vendruscolo (METHODS IN MOLECULAR BIOLOGY). - In: Biomolecular Simulations : Methods and Protocols / [a cura di] M. Bonomi, C. Camilloni. - Prima edizione. - [s.l] : Humana, New York, NY, 2019. - ISBN 9781493996087. - pp. 313-340 [10.1007/978-1-4939-9608-7_13]

A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference

C. Camilloni;M. Bonomi;
2019

Abstract

Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well as with system heterogeneity. Furthermore, metainference can be implemented using the metadynamics approach, which enables the computational study of complex biological systems requiring extensive conformational sampling. In this chapter, we provide a step-by-step guide to perform and analyse metadynamic metainference simulations using the ISDB module of the open-source PLUMED library, as well as a series of practical tips to avoid common mistakes. Specifically, we will guide the reader in the process of learning how to model the structural ensemble of a small disordered peptide by combining state-of-the-art molecular mechanics force fields with nuclear magnetic resonance data, including chemical shifts, scalar couplings and residual dipolar couplings.
Bayesian data modelling; Ensemble determination; Functional dynamics; Integrative modelling
Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin)
2019
Book Part (author)
File in questo prodotto:
File Dimensione Formato  
1901.08030.pdf

accesso riservato

Tipologia: Pre-print (manoscritto inviato all'editore)
Dimensione 1.68 MB
Formato Adobe PDF
1.68 MB Adobe PDF   Visualizza/Apri   Richiedi una copia
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/672289
Citazioni
  • ???jsp.display-item.citation.pmc??? 2
  • Scopus 4
  • ???jsp.display-item.citation.isi??? 3
social impact