A new force field (ECEPP-05) for peptides, proteins, and organic molecules

The Journal of Physical Chemistry. B
Yelena A ArnautovaHarold A Scheraga

Abstract

Parametrization and testing of a new all-atom force field for organic molecules and peptides with fixed bond lengths and bond angles are described. The van der Waals parameters for both the organic molecules and the peptides were taken from J. Phys. Chem. B 2003, 107, 7143 and J. Phys. Chem. B 2004, 108, 12181. First, the values of the 1-4 nonbonded and electrostatic scale factors appropriate to the new force field were determined by computing the conformational energies of six model molecules, namely, ethanol, ethylamine, propanol, propylamine, 1,2-ethanediol, and 1,3-propanediol with different values of these factors. The partial atomic charges of these molecules were obtained by fitting to the electrostatic potentials calculated with the HF/6-31G quantum-mechanical method. Two different charge models (single- and multiple-conformation-derived) were also considered. We demonstrated that the charge model has a stronger effect on the conformational energies than the 1-4 scaling. The choice of a charge model affected the conformational energies of even the smallest molecules considered, whereas the effect of the 1-4 electrostatic or nonbonded scaling was apparent only for 1,3-propanediol. The best agreement with high-level ab in...Continue Reading

References

Jul 20, 1973·Science·C B Anfinsen
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Oct 19, 2001·Proceedings of the National Academy of Sciences of the United States of America·J PillardyH A Scheraga
Apr 27, 2002·Acta Crystallographica. Section D, Biological Crystallography·Sven HovmöllerTomas Ohlson
Aug 1, 2002·Acta Crystallographica. Section B, Structural Science·W D Sam MotherwellDonald E Williams
Sep 19, 2002·Journal of the American Chemical Society·Carlos SimmerlingAdrian E Roitberg
Nov 8, 2002·Nature·Christopher D SnowMartin Gruebele
Dec 6, 2002·Journal of the American Chemical Society·Christopher D SnowVijay S Pande
Mar 14, 2003·Journal of Molecular Biology·Shibasish ChowdhuryYong Duan
Nov 26, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jorge A VilaHarold A Scheraga
Jul 21, 2004·Journal of Computational Chemistry·Alexander D Mackerell
Mar 9, 2005·Journal of Computational Chemistry·Eric J Sorin, Vijay S Pande
Aug 5, 2005·Proteins·Jorge A VilaHarold A Scheraga
Sep 28, 2005·Acta Crystallographica. Section B, Structural Science·G M DayP Verwer
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

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Sep 21, 2011·Physical Chemistry Chemical Physics : PCCP·Elizabeth A Ploetz, Paul E Smith
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jorge A VilaHarold A Scheraga
Dec 15, 2010·Journal of Biomolecular Structure & Dynamics·Simon Mitternacht, Igor N Berezovsky
Feb 22, 2013·The Journal of Chemical Physics·Yoshitake Sakae, Yuko Okamoto
Mar 25, 2010·The Journal of Chemical Physics·Satoshi OmoriAkinori Kidera
May 7, 2011·Annual Review of Biophysics·Harold A Scheraga
Jul 24, 2014·The Journal of Chemical Physics·Andreas Vitalis, Rohit V Pappu
Apr 2, 2010·Computational Optimization and Applications·Scott R McAllister, Christodoulos A Floudas
Feb 19, 2016·European Journal of Medicinal Chemistry·Andrey E ShchekotikhinMaria N Preobrazhenskaya
Oct 31, 2014·The Journal of Physical Chemistry. B·Chen-Yang ZhouYun-Dong Wu
Jan 8, 2008·Biophysical Journal·Liliana WroblewskaJeffrey Skolnick
Oct 30, 2007·Journal of Computational Chemistry·Kalju Kahn, Iiris Kahn
Oct 11, 2012·AIChE Journal·A SubramaniC A Floudas
Jul 6, 2013·Journal of Computational Chemistry·Steven K Burger, G Andrés Cisneros
Oct 7, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Muhammet E KöseGarry Rumbles
Feb 6, 2007·Biophysical Journal·Joanna MakowskaHarold A Scheraga
Apr 9, 2015·Quarterly Reviews of Biophysics·Harold A Scheraga
Sep 16, 2009·Biophysical Journal·Ashwin SubramaniChristodoulos A Floudas
Feb 5, 2015·The Journal of Physical Chemistry. a·Maxim V IvanovQadir K Timerghazin
Aug 1, 2016·Journal of Photochemistry and Photobiology. B, Biology·Nikita A DurandinMaria N Preobrazhenskaya
May 13, 2014·The Journal of Physical Chemistry. B·Fan JiangYun-Dong Wu
Feb 4, 2014·Journal of Chemical Theory and Computation·George A KhouryChristodoulos A Floudas
Apr 22, 2011·The Journal of Physical Chemistry. B·Albert Solernou, Juan Fernandez-Recio
Apr 20, 2017·The Journal of Antibiotics·Lyudmila N LysenkovaAndrey E Shchekotikhin
May 17, 2014·Journal of Computational Chemistry·Steven K BurgerJeremy Schofield
Sep 15, 2017·Physical Chemistry Chemical Physics : PCCP·Rafael B Frigori
Aug 4, 2018·Journal of Biomolecular Structure & Dynamics·Yana A ZabrodskayaVladimir V Egorov
Dec 7, 2018·Journal of Computer-aided Molecular Design·Pnina Dauber-Osguthorpe, A T Hagler
Mar 29, 2019·Protein Science : a Publication of the Protein Society·Gang XuJianpeng Ma
Jan 9, 2020·Organic & Biomolecular Chemistry·Ekaterina Y ChernikovaOlga A Fedorova
Sep 6, 2018·Current Medicinal Chemistry·Vladimir B SulimovAlexey V Sulimov
Oct 20, 2017·Protein Science : a Publication of the Protein Society·Gang XuJianpeng Ma
Feb 24, 2021·The Journal of Physical Chemistry. B·Boris S Zhorov
Jun 20, 2020·Journal of Chemical Theory and Computation·Jun PeiKenneth M Merz
Oct 11, 2011·Journal of Chemical Theory and Computation·Andreas P EichenbergerWilfred F van Gunsteren
Apr 12, 2017·Journal of Chemical Information and Modeling·Seungryong HeoJooyoung Lee
Jun 14, 2011·Journal of Chemical Theory and Computation·Da-Wei Li, Rafael Brüschweiler
Jan 16, 2020·The Journal of Physical Chemistry. B·Sung Bo HwangKyoung Tai No
Feb 7, 2019·Journal of Chemical Information and Modeling·Jun PeiKenneth M Merz

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