Literature DB >> 20440377

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber.

Tyler Luchko1, Sergey Gusarov, Daniel R Roe, Carlos Simmerling, David A Case, Jack Tuszynski, Andriy Kovalenko.   

Abstract

We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G.

Entities:  

Year:  2010        PMID： 20440377      PMCID： PMC2861832          DOI： 10.1021/ct900460m

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


  27 in total

1.  Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms.

Authors:  Danny Barash; Linjing Yang; Xiaoliang Qian; Tamar Schlick
Journal:  J Comput Chem       Date:  2003-01-15       Impact factor: 3.376

2.  All-atom structure prediction and folding simulations of a stable protein.

Authors:  Carlos Simmerling; Bentley Strockbine; Adrian E Roitberg
Journal:  J Am Chem Soc       Date:  2002-09-25       Impact factor: 15.419

3.  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Authors:  Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter Kollman
Journal:  J Comput Chem       Date:  2003-12       Impact factor: 3.376

4.  CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

Authors:  Sandeep Patel; Alexander D Mackerell; Charles L Brooks
Journal:  J Comput Chem       Date:  2004-09       Impact factor: 3.376

5.  Helical rosette nanotubes with tunable stability and hierarchy.

Authors:  Jesus G Moralez; Jose Raez; Takeshi Yamazaki; R Kishan Motkuri; Andriy Kovalenko; Hicham Fenniri
Journal:  J Am Chem Soc       Date:  2005-06-15       Impact factor: 15.419

6.  Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation.

Authors:  Takeshi Yamazaki; Takashi Imai; Fumio Hirata; Andriy Kovalenko
Journal:  J Phys Chem B       Date:  2007-02-08       Impact factor: 2.991

7.  Molecular basis for water-promoted supramolecular chirality inversion in helical rosette nanotubes.

Authors:  Ross S Johnson; Takeshi Yamazaki; Andriy Kovalenko; Hicham Fenniri
Journal:  J Am Chem Soc       Date:  2007-04-07       Impact factor: 15.419

8.  A molecular dynamics simulation study of segment B1 of protein G.

Authors:  F B Sheinerman; C L Brooks
Journal:  Proteins       Date:  1997-10

9.  A molecular site-site integral equation that yields the dielectric constant.

Authors:  Kippi M Dyer; John S Perkyns; George Stell; B Montgomery Pettitt
Journal:  J Chem Phys       Date:  2008-09-14       Impact factor: 3.488

10.  Localization of bound water in the solution structure of the immunoglobulin binding domain of streptococcal protein G. Evidence for solvent-induced helical distortion in solution.

Authors:  G M Clore; A M Gronenborn
Journal:  J Mol Biol       Date:  1992-02-20       Impact factor: 5.469
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  58 in total

1.  Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization.

Authors:  Nikolay Blinov; Lyudmyla Dorosh; David Wishart; Andriy Kovalenko
Journal:  Biophys J       Date:  2010-01-20       Impact factor: 4.033

2.  Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88.

Authors:  Juan Zeng; Yongxiu Li; John Z H Zhang; Ye Mei
Journal:  J Mol Model       Date:  2016-07-08       Impact factor: 1.810

3.  Multiscale methods for computational RNA enzymology.

Authors:  Maria T Panteva; Thakshila Dissanayake; Haoyuan Chen; Brian K Radak; Erich R Kuechler; George M Giambaşu; Tai-Sung Lee; Darrin M York
Journal:  Methods Enzymol       Date:  2015-01-22       Impact factor: 1.600

4.  Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution.

Authors:  Julija Zavadlav; Jurij Sablić; Rudolf Podgornik; Matej Praprotnik
Journal:  Biophys J       Date:  2018-04-09       Impact factor: 4.033

5.  Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects.

Authors:  Hiraku Oshima; Tomohiko Hayashi; Masahiro Kinoshita
Journal:  Biophys J       Date:  2016-06-07       Impact factor: 4.033

6.  Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids.

Authors:  Hung T Nguyen; Suzette A Pabit; Steve P Meisburger; Lois Pollack; David A Case
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

7.  A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase.

Authors:  Jiraphorn Phanich; Thanyada Rungrotmongkol; Daniel Sindhikara; Saree Phongphanphanee; Norio Yoshida; Fumio Hirata; Nawee Kungwan; Supot Hannongbua
Journal:  Protein Sci       Date:  2015-06-22       Impact factor: 6.725

8.  Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions.

Authors:  In Suk Joung; Tyler Luchko; David A Case
Journal:  J Chem Phys       Date:  2013-01-28       Impact factor: 3.488

9.  Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition.

Authors:  Tomohiko Hayashi; Hiraku Oshima; Tsukasa Mashima; Takashi Nagata; Masato Katahira; Masahiro Kinoshita
Journal:  Nucleic Acids Res       Date:  2014-05-06       Impact factor: 16.971

10.  Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.

Authors:  Omar Awile; Anita Krisko; Ivo F Sbalzarini; Bojan Zagrovic
Journal:  PLoS Comput Biol       Date:  2010-07-15       Impact factor: 4.475
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