Literature DB >> 10368306

New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations.

T Darden1, L Perera, L Li, L Pedersen.   

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Year:  1999        PMID： 10368306     DOI： 10.1016/s0969-2126(99)80033-1

Source DB:  PubMed          Journal:  Structure        ISSN： 0969-2126            Impact factor:   5.006


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  179 in total

1.  Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment.

Authors:  D R Bevan; L Li; L G Pedersen; T A Darden
Journal:  Biophys J       Date:  2000-02       Impact factor: 4.033

2.  On the truncation of long-range electrostatic interactions in DNA.

Authors:  J Norberg; L Nilsson
Journal:  Biophys J       Date:  2000-09       Impact factor: 4.033

3.  Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.

Authors:  Yongping Pan; Alexander D MacKerell
Journal:  Nucleic Acids Res       Date:  2003-12-15       Impact factor: 16.971

4.  Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties.

Authors:  Masakazu Sekijima; Chie Motono; Satoshi Yamasaki; Kiyotoshi Kaneko; Yutaka Akiyama
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

5.  Molecular dynamics studies of the 3D structure and planar ligand binding of a quadruplex dimer.

Authors:  Ming-Hui Li; Quan Luo; Xiang-Gui Xue; Ze-Sheng Li
Journal:  J Mol Model       Date:  2010-05-29       Impact factor: 1.810

6.  Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient.

Authors:  Junmei Wang; Tingjun Hou
Journal:  J Comput Chem       Date:  2011-09-22       Impact factor: 3.376

7.  Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.

Authors:  Loïc Etheve; Juliette Martin; Richard Lavery
Journal:  Nucleic Acids Res       Date:  2015-12-31       Impact factor: 16.971

8.  Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin.

Authors:  Mathew Varghese Koonammackal; Unnikrishnan Viswambharan Nair Nellipparambil; Chellappanpillai Sudarsanakumar
Journal:  J Mol Model       Date:  2011-02-02       Impact factor: 1.810

9.  Methyl-methoxylpyrrolinone and flavinium nucleus binding signatures on falcipain-2 active site.

Authors:  Olaposi I Omotuyi
Journal:  J Mol Model       Date:  2014-08-06       Impact factor: 1.810

10.  Crystal structure and mode of helicase binding of the C-terminal domain of primase from Helicobacter pylori.

Authors:  Syed Arif Abdul Rehman; Vijay Verma; Mohit Mazumder; Suman K Dhar; S Gourinath
Journal:  J Bacteriol       Date:  2013-04-12       Impact factor: 3.490
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