Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure

Protein Sci. 2021 Jan;30(1):250-261. doi: 10.1002/pro.3995. Epub 2020 Dec 3.


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 (

Keywords: biophysics; chemical cross-linking; electron microscopy; integrative structure modeling; model validation; protein complexes; structural biology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Validation Study

MeSH terms

  • Databases, Protein*
  • Models, Molecular*
  • Multiprotein Complexes / chemistry*
  • Protein Structure, Quaternary
  • Software*


  • Multiprotein Complexes