Preprint Review Version 1 This version is not peer-reviewed

Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields

Version 1 : Received: 13 December 2018 / Approved: 17 December 2018 / Online: 17 December 2018 (10:54:32 CET)

A peer-reviewed article of this Preprint also exists.

Ciemny, M.P.; Badaczewska-Dawid, A.E.; Pikuzinska, M.; Kolinski, A.; Kmiecik, S. Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields. Int. J. Mol. Sci. 2019, 20, 606. Ciemny, M.P.; Badaczewska-Dawid, A.E.; Pikuzinska, M.; Kolinski, A.; Kmiecik, S. Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields. Int. J. Mol. Sci. 2019, 20, 606.

Journal reference: Int. J. Mol. Sci. 2019, 20, 606
DOI: 10.3390/ijms20030606

Abstract

The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling disordered protein interactions and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein-peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein-peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution and studies of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.

Subject Areas

coarse-grained; CABS model; MC simulations; statistical force fields; disordered protein; protein structure

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