Evaluation and Selection of Dynamic Protein Structural Ensembles with CoNSEnsX

Methods Mol Biol. 2020:2112:241-254. doi: 10.1007/978-1-0716-0270-6_16.

Abstract

Understanding protein function at atomistic detail is not possible without accounting for the internal dynamics of these molecules. Ensemble-based models are based on the premise that single conformers cannot account for all experimental observations on the given molecule. Rather, a suitable set of structures, representing the internal dynamics of the protein at a given timescale, are necessary to achieve correspondence to measurements. CoNSEnsX+ is a service specifically designed for the investigation of such ensembles for compliance with NMR-derived parameters. In contrast to common structure evaluation tools, all parameters are treated as an average over the ensemble, if are not themselves an ensemble property like order parameters. CoNSEnsX+ is also capable of selecting a sub-ensemble with increased correspondence to a set of user-defined experimental parameters. CoNSEnsX+ is available as a web server at http://consensx.itk.ppke.hu , and the full Python source code is available on GitHub.

Keywords: Chemical shift; Ensemble selection; NMR spectroscopy; Order parameter; Protein internal dynamics; Residual dipolar coupling; Scalar coupling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Molecular Docking Simulation / methods*
  • Molecular Dynamics Simulation
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Conformation*
  • Proteins / chemistry*
  • Software

Substances

  • Proteins