Literature DB >> 34845616

Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.

Vinícius G Contessoto1, Vinícius M de Oliveira2,3, Vitor B P Leite4.   

Abstract

Computational coarse-grained models play a fundamental role as a research tool in protein folding, and they are important in bridging theory and experiments. Folding mechanisms are generally discussed using the energy landscape framework, which is well mapped within a class of simplified structure-based models. In this chapter, simplified computer models are discussed with special focus on structure-based ones.
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Energy landscapes; Molecular dynamics; Structure-based models

Mesh:

Year:  2022        PMID: 34845616     DOI: 10.1007/978-1-0716-1716-8_16

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  62 in total

1.  Protein tertiary structure recognition using optimized Hamiltonians with local interactions.

Authors:  R A Goldstein; Z A Luthey-Schulten; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1992-10-01       Impact factor: 11.205

2.  Comparing folding codes for proteins and polymers.

Authors:  H S Chan; K A Dill
Journal:  Proteins       Date:  1996-03

3.  Capturing transition paths and transition states for conformational rearrangements in the ribosome.

Authors:  Jeffrey K Noel; Jorge Chahine; Vitor B P Leite; Paul Charles Whitford
Journal:  Biophys J       Date:  2014-12-16       Impact factor: 4.033

Review 4.  Challenges in describing ribosome dynamics.

Authors:  Kien Nguyen; Paul Charles Whitford
Journal:  Phys Biol       Date:  2017-03-22       Impact factor: 2.583

5.  Physics transforming the life sciences.

Authors:  José N Onuchic
Journal:  Phys Biol       Date:  2014-10-08       Impact factor: 2.583

6.  Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.

Authors:  Susmita Roy; José N Onuchic; Karissa Y Sanbonmatsu
Journal:  Biophys J       Date:  2017-07-25       Impact factor: 4.033

7.  Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones.

Authors:  Haiqing Zhao; David Winogradoff; Minh Bui; Yamini Dalal; Garegin A Papoian
Journal:  J Am Chem Soc       Date:  2016-08-12       Impact factor: 15.419

8.  Spin glasses and the statistical mechanics of protein folding.

Authors:  J D Bryngelson; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1987-11       Impact factor: 11.205

9.  Biomolecular dynamics: order-disorder transitions and energy landscapes.

Authors:  Paul C Whitford; Karissa Y Sanbonmatsu; José N Onuchic
Journal:  Rep Prog Phys       Date:  2012-06-28

10.  De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.

Authors:  Michele Di Pierro; Ryan R Cheng; Erez Lieberman Aiden; Peter G Wolynes; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-31       Impact factor: 11.205

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