Literature DB >> 21526232

Multiscale modeling of biological functions.

Shina Caroline Lynn Kamerlin1, Arieh Warshel.   

Abstract

Recent years have witnessed a tremendous explosion in computational power, which in turn has resulted in great progress in the complexity of the biological and chemical problems that can be addressed by means of all-atom simulations. Despite this, however, our computational time is not infinite, and in fact many of the key problems of the field were resolved long before the existence of the current levels of computational power. This review will start by presenting a brief historical overview of the use of multiscale simulations in biology, and then present some key developments in the field, highlighting several cases where the use of a physically sound simplification is clearly superior to a brute-force approach. Finally, some potential future directions will be discussed. This journal is © the Owner Societies 2011

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Year:  2011        PMID: 21526232      PMCID: PMC3102780          DOI: 10.1039/c0cp02823a

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  76 in total

1.  Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

Authors:  Vijay S Pande; Ian Baker; Jarrod Chapman; Sidney P Elmer; Siraj Khaliq; Stefan M Larson; Young Min Rhee; Michael R Shirts; Christopher D Snow; Eric J Sorin; Bojan Zagrovic
Journal:  Biopolymers       Date:  2003-01       Impact factor: 2.505

2.  Escaping free-energy minima.

Authors:  Alessandro Laio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-23       Impact factor: 11.205

Review 3.  The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations.

Authors:  Mitsunori Kato; Andrei V Pisliakov; Arieh Warshel
Journal:  Proteins       Date:  2006-09-01

Review 4.  Recent successes of the energy landscape theory of protein folding and function.

Authors:  P G Wolynes
Journal:  Q Rev Biophys       Date:  2005-11       Impact factor: 5.318

5.  Exploring the role of large conformational changes in the fidelity of DNA polymerase beta.

Authors:  Yun Xiang; Myron F Goodman; William A Beard; Samuel H Wilson; Arieh Warshel
Journal:  Proteins       Date:  2008-01-01

6.  Conserved residues and the mechanism of protein folding.

Authors:  E Shakhnovich; V Abkevich; O Ptitsyn
Journal:  Nature       Date:  1996-01-04       Impact factor: 49.962

7.  Constant pH molecular dynamics with proton tautomerism.

Authors:  Jana Khandogin; Charles L Brooks
Journal:  Biophys J       Date:  2005-04-29       Impact factor: 4.033

8.  Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models.

Authors:  Benjamin M Messer; Maite Roca; Zhen T Chu; Spyridon Vicatos; Alexandra Vardi Kilshtain; Arieh Warshel
Journal:  Proteins       Date:  2010-04

9.  Phospholipid component volumes: determination and application to bilayer structure calculations.

Authors:  R S Armen; O D Uitto; S E Feller
Journal:  Biophys J       Date:  1998-08       Impact factor: 4.033

10.  Toward accurate screening in computer-aided enzyme design.

Authors:  Maite Roca; Alexandra Vardi-Kilshtain; Arieh Warshel
Journal:  Biochemistry       Date:  2009-04-14       Impact factor: 3.162

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  15 in total

1.  Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions.

Authors:  Jerônimo Lameira; Ilya Kupchencko; Arieh Warshel
Journal:  J Phys Chem B       Date:  2016-02-29       Impact factor: 2.991

2.  Quantum-chemical approach to determining the high potency of clorgyline as an irreversible acetylenic monoamine oxidase inhibitor.

Authors:  Matic Pavlin; Janez Mavri; Matej Repič; Robert Vianello
Journal:  J Neural Transm (Vienna)       Date:  2013-04-02       Impact factor: 3.575

Review 3.  Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.

Authors:  Arieh Warshel; Ram Prasad Bora
Journal:  J Chem Phys       Date:  2016-05-14       Impact factor: 3.488

Review 4.  Recent advances in transferable coarse-grained modeling of proteins.

Authors:  Parimal Kar; Michael Feig
Journal:  Adv Protein Chem Struct Biol       Date:  2014-08-24       Impact factor: 3.507

Review 5.  Why nature really chose phosphate.

Authors:  Shina C L Kamerlin; Pankaz K Sharma; Ram B Prasad; Arieh Warshel
Journal:  Q Rev Biophys       Date:  2013-01-15       Impact factor: 5.318

6.  Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.

Authors:  Parimal Kar; Michael Feig
Journal:  J Chem Theory Comput       Date:  2017-10-19       Impact factor: 6.006

7.  Virtual eyes for technology and cultural heritage: toward computational strategy for new and old indigo-based dyes.

Authors:  Vincenzo Barone; Malgorzata Biczysko; Camille Latouche; Andrea Pasti
Journal:  Theor Chem Acc       Date:  2015-11-11       Impact factor: 1.702

8.  Conductance selectivity of Na+ across the K+ channel via Na+ trapped in a tortuous trajectory.

Authors:  Kenichiro Mita; Takashi Sumikama; Masayuki Iwamoto; Yuka Matsuki; Kenji Shigemi; Shigetoshi Oiki
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-23       Impact factor: 12.779

Review 9.  Recent advances in design and applications of biomimetic self-assembled peptide hydrogels for hard tissue regeneration.

Authors:  Haniyeh Najafi; Mahboobeh Jafari; Ghazal Farahavar; Samira Sadat Abolmaali; Negar Azarpira; Sedigheh Borandeh; Raheleh Ravanfar
Journal:  Biodes Manuf       Date:  2021-07-20

10.  Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex.

Authors:  Fu-Feng Liu; Bo Huang; Xiao-Yan Dong; Yan Sun
Journal:  PLoS One       Date:  2013-06-12       Impact factor: 3.240

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