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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Integrative structural and dynamical biology with PLUMED-ISDB.

Massimiliano Bonomi1, Carlo Camilloni2,3

  • 1Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.

Bioinformatics (Oxford, England)
|September 30, 2017
PubMed
Summary

PLUMED-ISDB integrates experimental data with prior knowledge for accurate biomolecular structural modeling. This open-source tool enhances the determination of structure and dynamics in complex biological systems.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Accurate structural models are crucial for understanding biological systems.
  • Integrating experimental data with physico-chemical knowledge is essential for robust modeling.
  • Conformationally heterogeneous systems present significant modeling challenges.

Purpose of the Study:

  • To present PLUMED-ISDB, an open-source module for the PLUMED library.
  • To enable simultaneous determination of structure and dynamics for complex biological systems.
  • To integrate diverse experimental data with a priori information using a Bayesian framework.

Main Methods:

  • Utilizes metainference, a Bayesian framework, for data integration.
  • Incorporates various experimental observables including NMR, FRET, SAXS, and cryo-EM data.
  • Leverages enhanced sampling methods for modeling at different resolutions.

Main Results:

  • PLUMED-ISDB allows simultaneous structure and dynamics determination.
  • The module effectively integrates experimental data with prior physico-chemical knowledge.
  • It accounts for noise and ensemble-averaged nature of experimental data.

Conclusions:

  • Accurate structural models can be achieved by combining experimental data with prior knowledge.
  • PLUMED-ISDB provides a versatile platform for modeling diverse biological systems.
  • The open-source module facilitates advanced structural and dynamic analyses.