Using Integrative Modeling Platform to compute,validate, and archive a model of a protein complex structure |
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| Authors: | Daniel J. Saltzberg Shruthi Viswanath Ignacia Echeverria Ilan E. Chemmama Ben Webb Andrej Sali |
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| Affiliation: | 1. Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco California, USA ; 2. National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore India ; 3. Department of Cellular and Molecular Pharmacology, University of California, San Francisco California, USA |
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| Abstract: | Biology is advanced by producing structural models of biological systems, such as protein complexes. Some systems are recalcitrant to traditional structure determination methods. In such cases, it may still be possible to produce useful models by integrative structure determination that depends on simultaneous use of multiple types of data. An ensemble of models that are sufficiently consistent with the data is produced by a structural sampling method guided by a data‐dependent scoring function. The variation in the ensemble of models quantified the uncertainty of the structure, generally resulting from the uncertainty in the input information and actual structural heterogeneity in the samples used to produce the data. Here, we describe how to generate, assess, and interpret ensembles of integrative structural models using our open source Integrative Modeling Platform program ( https://integrativemodeling.org ). |
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| Keywords: | biophysics chemical cross‐linking electron microscopy integrative structure modeling model validation protein complexes structural biology |
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