Literature DB >> 26874473

Perspective: Computer simulations of long time dynamics.

Ron Elber1.   

Abstract

Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.

Mesh:

Year:  2016        PMID: 26874473      PMCID: PMC4752541          DOI: 10.1063/1.4940794

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  69 in total

Review 1.  Fast kinetics and mechanisms in protein folding.

Authors:  W A Eaton; V Muñoz; S J Hagen; G S Jas; L J Lapidus; E R Henry; J Hofrichter
Journal:  Annu Rev Biophys Biomol Struct       Date:  2000

2.  An atomically detailed study of the folding pathways of protein A with the stochastic difference equation.

Authors:  Avijit Ghosh; Ron Elber; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2002-07-24       Impact factor: 11.205

3.  Computing time scales from reaction coordinates by milestoning.

Authors:  Anton K Faradjian; Ron Elber
Journal:  J Chem Phys       Date:  2004-06-15       Impact factor: 3.488

4.  Coarse master equations for peptide folding dynamics.

Authors:  Nicolae-Viorel Buchete; Gerhard Hummer
Journal:  J Phys Chem B       Date:  2008-01-31       Impact factor: 2.991

5.  Rate constant and reaction coordinate of Trp-cage folding in explicit water.

Authors:  Jarek Juraszek; Peter G Bolhuis
Journal:  Biophys J       Date:  2008-08-01       Impact factor: 4.033

6.  Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

Authors:  Victor Ovchinnikov; Martin Karplus; Eric Vanden-Eijnden
Journal:  J Chem Phys       Date:  2011-02-28       Impact factor: 3.488

7.  Weighted-ensemble Brownian dynamics simulations for protein association reactions.

Authors:  G A Huber; S Kim
Journal:  Biophys J       Date:  1996-01       Impact factor: 4.033

8.  Milestoning with coarse memory.

Authors:  Alexander T Hawk
Journal:  J Chem Phys       Date:  2013-04-21       Impact factor: 3.488

9.  Kinetics of cytochrome C folding: atomically detailed simulations.

Authors:  Alfredo E Cárdenas; Ron Elber
Journal:  Proteins       Date:  2003-05-01

10.  How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations.

Authors:  Serdal Kirmizialtin; Virginia Nguyen; Kenneth A Johnson; Ron Elber
Journal:  Structure       Date:  2012-04-03       Impact factor: 5.006

View more
  10 in total

1.  Life in silico: Are we close yet?

Authors:  Dmitrii E Makarov
Journal:  Proc Natl Acad Sci U S A       Date:  2021-02-16       Impact factor: 11.205

2.  The allosteric switching mechanism in bacteriophage MS2.

Authors:  Matthew R Perkett; Dina T Mirijanian; Michael F Hagan
Journal:  J Chem Phys       Date:  2016-07-21       Impact factor: 3.488

3.  Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: a molecular modeling and dynamics approach.

Authors:  Ashish Kumar Agrahari; Meghana Muskan; C George Priya Doss; R Siva; Hatem Zayed
Journal:  Metab Brain Dis       Date:  2018-05-27       Impact factor: 3.584

4.  Molecular latent space simulators.

Authors:  Hythem Sidky; Wei Chen; Andrew L Ferguson
Journal:  Chem Sci       Date:  2020-08-26       Impact factor: 9.825

5.  Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins.

Authors:  Stanislav M Avdoshenko; Atanu Das; Rohit Satija; Garegin A Papoian; Dmitrii E Makarov
Journal:  Sci Rep       Date:  2017-03-21       Impact factor: 4.379

6.  Finding multiple reaction pathways via global optimization of action.

Authors:  Juyong Lee; In-Ho Lee; InSuk Joung; Jooyoung Lee; Bernard R Brooks
Journal:  Nat Commun       Date:  2017-05-26       Impact factor: 14.919

7.  Mechanistic insights into the deleterious roles of Nasu-Hakola disease associated TREM2 variants.

Authors:  Raju Dash; Ho Jin Choi; Il Soo Moon
Journal:  Sci Rep       Date:  2020-02-27       Impact factor: 4.379

8.  Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein.

Authors:  Lenka Stejskal; William D Lees; David S Moss; Machaela Palor; Richard J Bingham; Adrian J Shepherd; Joe Grove
Journal:  PLoS Comput Biol       Date:  2020-02-28       Impact factor: 4.475

9.  The impact of missense mutation in PIGA associated to paroxysmal nocturnal hemoglobinuria and multiple congenital anomalies-hypotonia-seizures syndrome 2: A computational study.

Authors:  Ashish Kumar Agrahari; Enrico Pieroni; Gianluca Gatto; Amit Kumar
Journal:  Heliyon       Date:  2019-10-23

10.  Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank.

Authors:  Emanuel K Peter; Jiri Cerny
Journal:  Int J Mol Sci       Date:  2018-10-30       Impact factor: 5.923

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.