Literature DB >> 10322213

Protein dynamics simulations from nanoseconds to microseconds.

S Doniach1, P Eastman.   

Abstract

There have been a number of advances in atomic resolution simulations of biomolecules during the past few years. These have arisen partly from improvements to computer power and partly from algorithmic improvements. There have also been advances in measuring time-dependent fluctuations in proteins using NMR spectroscopy, revealing the importance of fluctuations in the microsecond to millisecond time range. Progress has also been made in measuring how far the simulations are able to represent the accessible phase space that is available to the protein in its native state, in solution, at room temperature. Another area of development is the simulation of protein unfolding at atomic resolution.

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Year:  1999        PMID: 10322213     DOI: 10.1016/S0959-440X(99)80022-0

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  11 in total

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2.  Molecular dynamics simulations of peptides and proteins with amplified collective motions.

Authors:  Zhiyong Zhang; Yunyu Shi; Haiyan Liu
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

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4.  A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations.

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Journal:  J Struct Biol       Date:  2006-11-10       Impact factor: 2.867

Review 5.  Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.

Authors:  Ivet Bahar; Timothy R Lezon; Ahmet Bakan; Indira H Shrivastava
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6.  Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.

Authors:  D J Cashman; A B Mamonov; D Bhatt; D M Zuckerman
Journal:  Curr Top Med Chem       Date:  2011       Impact factor: 3.295

7.  Iterative cluster-NMA: A tool for generating conformational transitions in proteins.

Authors:  Adam D Schuyler; Robert L Jernigan; Pradman K Qasba; Boopathy Ramakrishnan; Gregory S Chirikjian
Journal:  Proteins       Date:  2009-02-15

8.  Chemical composition and pharmacological mechanism of ephedra-glycyrrhiza drug pair against coronavirus disease 2019 (COVID-19).

Authors:  Xiaoling Li; Qin Qiu; Mingyue Li; Haowen Lin; Shilin Cao; Qu Wang; Zishi Chen; Wenhao Jiang; Wen Zhang; Yuge Huang; Hui Luo; Lianxiang Luo
Journal:  Aging (Albany NY)       Date:  2021-02-13       Impact factor: 5.682

9.  Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family.

Authors:  Dennis R Livesay; Dang H Huynh; Sargis Dallakyan; Donald J Jacobs
Journal:  Chem Cent J       Date:  2008-08-12       Impact factor: 4.215

10.  The natural way forward: Molecular dynamics simulation analysis of phytochemicals from Indian medicinal plants as potential inhibitors of SARS-CoV-2 targets.

Authors:  Pratap Kumar Parida; Dipak Paul; Debamitra Chakravorty
Journal:  Phytother Res       Date:  2020-09-24       Impact factor: 6.388

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