Determining Protein Complex Structures Based on a Bayesian Model of in Vivo Förster Resonance Energy Transfer (FRET) Data
Massimiliano Bonomi,Massimiliano Bonomi,Riccardo Pellarin,Seung Joong Kim,Daniel Russel,Bryan A. Sundin,Michael Riffle,Daniel Jaschob,Richard Ramsden,Trisha N. Davis,Eric G D Muller,Andrej Sali +11 more
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TL;DR: The Bayesian approach to determine macromolecular structures through a combination of in vivo FRETR data and data from other sources, such as electron microscopy and chemical cross-linking is implemented in the open-source Integrative Modeling Platform.
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About: This article is published in Molecular & Cellular Proteomics. The article was published on 01 Nov 2014. and is currently open access. The article focuses on the topics: Posterior probability.
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Citations
Inferential Structure Determination
Wolfgang Rieping,Michael Habeck +1 more
- 01 Aug 2004
TL;DR: In this paper, the authors used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision, and implemented this approach by using Markov chain Monte Carlo techniques.
282
Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems
Mykola Dimura,Thomas Peulen,Christian A. Hanke,Aiswaria Prakash,Holger Gohlke,Claus A. M. Seidel +5 more
TL;DR: A workflow that automates integrative structural modeling and experiment planning to put hybrid-FRET on rails is presented and procedures to incorporate prior structural knowledge and to obtain optimal distance networks are discussed.
191
Uncertainty in integrative structural modeling.
TL;DR: Integrative structural modeling uses multiple types of input information and proceeds in four stages: gathering information, designing model representation and converting information into a scoring function, sampling good-scoring models, and analyzing models and information.
110
Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics.
TL;DR: To exhaustively and efficiently generate structural ensembles, metainference is combined with metadynamics and its application to the calculation of the free energy landscape of the alanine dipeptide is illustrated.
97
Integrative Modelling of Biomolecular Complexes.
TL;DR: This review highlights recent works that exemplify how the use of integrative and/or information-driven approaches and platforms can produce highly accurate structural models, including systems which present many challenges when studied with traditional structural biology techniques.
87
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