Literature DB >> 23354627

Limiting assumptions in molecular modeling: electrostatics.

Garland R Marshall1.   

Abstract

Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

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Year:  2013        PMID: 23354627      PMCID: PMC3594449          DOI: 10.1007/s10822-013-9634-x

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  71 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

Review 2.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

3.  Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.

Authors:  C Pérez; M Pastor; A R Ortiz; F Gago
Journal:  J Med Chem       Date:  1998-03-12       Impact factor: 7.446

4.  Markov state model reveals folding and functional dynamics in ultra-long MD trajectories.

Authors:  Thomas J Lane; Gregory R Bowman; Kyle Beauchamp; Vincent A Voelz; Vijay S Pande
Journal:  J Am Chem Soc       Date:  2011-10-26       Impact factor: 15.419

Review 5.  Aromatic rings in chemical and biological recognition: energetics and structures.

Authors:  Laura M Salonen; Manuel Ellermann; François Diederich
Journal:  Angew Chem Int Ed Engl       Date:  2011-04-28       Impact factor: 15.336

6.  The matching of electrostatic extrema: a useful method in drug design? A study of phosphodiesterase III inhibitors.

Authors:  R P Apaya; B Lucchese; S L Price; J G Vinter
Journal:  J Comput Aided Mol Des       Date:  1995-02       Impact factor: 3.686

7.  Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation.

Authors:  Jennie L Thomas; Douglas J Tobias; Alexander D Mackerell
Journal:  J Phys Chem B       Date:  2007-10-24       Impact factor: 2.991

8.  Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations.

Authors:  Alexandre V Morozov; Tanja Kortemme; Kiril Tsemekhman; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-26       Impact factor: 11.205

9.  Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme-substrate complex: influenza neuraminidase inhibition.

Authors:  Paulina M Dominiak; Anatoliy Volkov; Adam P Dominiak; Katarzyna N Jarzembska; Philip Coppens
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-04-18

10.  The future of molecular dynamics simulations in drug discovery.

Authors:  David W Borhani; David E Shaw
Journal:  J Comput Aided Mol Des       Date:  2011-12-20       Impact factor: 3.686

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  6 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

Review 2.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

3.  Structure-based stabilization of insulin as a therapeutic protein assembly via enhanced aromatic-aromatic interactions.

Authors:  Nischay K Rege; Nalinda P Wickramasinghe; Alisar N Tustan; Nelson F B Phillips; Vivien C Yee; Faramarz Ismail-Beigi; Michael A Weiss
Journal:  J Biol Chem       Date:  2018-06-07       Impact factor: 5.157

4.  Calculating the sensitivity and robustness of binding free energy calculations to force field parameters.

Authors:  Gabriel J Rocklin; David L Mobley; Ken A Dill
Journal:  J Chem Theory Comput       Date:  2013-07-09       Impact factor: 6.006

5.  Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding.

Authors:  Luciano A Abriata; Matteo Dal Peraro
Journal:  Sci Rep       Date:  2015-05-29       Impact factor: 4.379

6.  Evaluation of CM5 Charges for Condensed-Phase Modeling.

Authors:  Jonah Z Vilseck; Julian Tirado-Rives; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2014-04-01       Impact factor: 6.006

  6 in total

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