Literature DB >> 23981057

Classical electrostatics for biomolecular simulations.

G Andrés Cisneros1, Mikko Karttunen, Pengyu Ren, Celeste Sagui.   

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Year:  2013        PMID： 23981057      PMCID： PMC3947274          DOI： 10.1021/cr300461d

Source DB:  PubMed          Journal:  Chem Rev        ISSN： 0009-2665            Impact factor:   60.622


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  292 in total

1.  Ion solvation thermodynamics from simulation with a polarizable force field.

Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

2.  Distributed Multipole Analysis:  Stability for Large Basis Sets.

Authors:  Anthony J Stone
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

3.  Validation of the 53A6 GROMOS force field.

Authors:  Chris Oostenbrink; Thereza A Soares; Nico F A van der Vegt; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2005-04-01       Impact factor: 1.733

4.  Gd(III) polyaminocarboxylate chelate: realistic many-body molecular dynamics simulations for molecular imaging applications.

Authors:  Carine Clavaguéra; Emmanuelle Sansot; Florent Calvo; Jean-Pierre Dognon
Journal:  J Phys Chem B       Date:  2006-07-06       Impact factor: 2.991

5.  Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics.

Authors:  Christopher J Fennell; J Daniel Gezelter
Journal:  J Chem Phys       Date:  2006-06-21       Impact factor: 3.488

6.  Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure.

Authors:  Volodymyr Babin; Jason Baucom; Thomas A Darden; Celeste Sagui
Journal:  J Phys Chem B       Date:  2006-06-15       Impact factor: 2.991

7.  The spatial structure in liquid water.

Authors:  P G Kusalik; I M Svishchev
Journal:  Science       Date:  1994-08-26       Impact factor: 47.728

8.  Stabilization of the purine.purine.pyrimidine DNA base triplets by divalent metal cations.

Authors:  J Sponer; M Sabat; J V Burda; A M Doody; J Leszczynski; P Hobza
Journal:  J Biomol Struct Dyn       Date:  1998-08

9.  Constant pH molecular dynamics with proton tautomerism.

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

10.  Exploring ion permeation energetics in gramicidin A using polarizable charge equilibration force fields.

Authors:  Sandeep Patel; Joseph E Davis; Brad A Bauer
Journal:  J Am Chem Soc       Date:  2009-10-07       Impact factor: 15.419
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  48 in total

1.  Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors.

Authors:  Dejun Lin
Journal:  J Chem Phys       Date:  2015-09-21       Impact factor: 3.488

2.  A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations.

Authors:  Dong Fang; Robert E Duke; G Andrés Cisneros
Journal:  J Chem Phys       Date:  2015-07-28       Impact factor: 3.488

3.  Efficient treatment of induced dipoles.

Authors:  Andrew C Simmonett; Frank C Pickard; Yihan Shao; Thomas E Cheatham; Bernard R Brooks
Journal:  J Chem Phys       Date:  2015-08-21       Impact factor: 3.488

4.  LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Authors:  Eric G Kratz; Alice R Walker; Louis Lagardère; Filippo Lipparini; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Comput Chem       Date:  2016-01-18       Impact factor: 3.376

5.  An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Authors:  Jing Huang; Ye Mei; Gerhard König; Andrew C Simmonett; Frank C Pickard; Qin Wu; Lee-Ping Wang; Alexander D MacKerell; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2017-01-24       Impact factor: 6.006

Review 6.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

Review 7.  Molecular Dynamics Simulations of Membrane Permeability.

Authors:  Richard M Venable; Andreas Krämer; Richard W Pastor
Journal:  Chem Rev       Date:  2019-02-12       Impact factor: 60.622

Review 8.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

9.  Polarizable molecular dynamics in a polarizable continuum solvent.

Authors:  Filippo Lipparini; Louis Lagardère; Christophe Raynaud; Benjamin Stamm; Eric Cancès; Benedetta Mennucci; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

10.  Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.

Authors:  Louis Lagardère; Filippo Lipparini; Étienne Polack; Benjamin Stamm; Éric Cancès; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2014-02-28       Impact factor: 6.006
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