Literature DB >> 17406086

Comment on elastic network models and proteins.

M F Thorpe1.   

Abstract

Elastic network models have been used to study the properties of coarse grained models of proteins and larger biomolecular complexes. In this comment, we point out that it is important to build rotational symmetry, as well as translational symmetry, into these models that are designed to describe the rigidity, and the associated low-frequency deformations. This leads to strong restrictions on what form of interactions can be used. In particular, the only allowed two-center harmonic interactions are those corresponding to Hooke springs. Additional complexity can be introduced if required by using three-center harmonic interactions.

Entities:  

Mesh:

Substances:

Year:  2007        PMID: 17406086     DOI: 10.1088/1478-3975/4/1/N01

Source DB:  PubMed          Journal:  Phys Biol        ISSN: 1478-3967            Impact factor:   2.583


  6 in total

1.  Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models.

Authors:  Lee-Wei Yang
Journal:  Biophys J       Date:  2011-04-06       Impact factor: 4.033

Review 2.  Global dynamics of proteins: bridging between structure and function.

Authors:  Ivet Bahar; Timothy R Lezon; Lee-Wei Yang; Eran Eyal
Journal:  Annu Rev Biophys       Date:  2010       Impact factor: 12.981

Review 3.  Computational models of protein kinematics and dynamics: beyond simulation.

Authors:  Bryant Gipson; David Hsu; Lydia E Kavraki; Jean-Claude Latombe
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2012-04-09       Impact factor: 10.745

4.  Tracing conformational changes in proteins.

Authors:  Nurit Haspel; Mark Moll; Matthew L Baker; Wah Chiu; Lydia E Kavraki
Journal:  BMC Struct Biol       Date:  2010-05-17

5.  Generalized spring tensor models for protein fluctuation dynamics and conformation changes.

Authors:  Tu-Liang Lin; Guang Song
Journal:  BMC Struct Biol       Date:  2010-05-17

6.  Using Spectral Representation to Classify Proteins' Conformational States.

Authors:  Seyed Majid Saberi Fathi; Jack A Tuszynski
Journal:  Int J Mol Sci       Date:  2018-07-18       Impact factor: 5.923

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.