PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK II: COMPARISONS OF FORCE FIELDS BY FOLDING SIMULATIONS OF SHORT PEPTIDES
2004 ◽
Vol 03
(03)
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pp. 359-378
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Keyword(s):
In Paper I of this series, the formulations of the optimization method of existing force-field parameters for protein systems have been presented. We then applied it to five sets of force-field parameters, namely, AMBER parm94, AMBER parm96, AMBER parm99, CHARMM version 22, and OPLS-AA. In order to test the validity of these force fields, the folding simulations of α-helical and β-hairpin peptides have been performed with each of the original and optimized force-field parameters. We found that all five modified force-field parameters gave both α-helical and β-hairpin structures more consistent with the experimental implications than the original force fields.
2004 ◽
Vol 03
(03)
◽
pp. 339-358
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Keyword(s):
2003 ◽
Vol 382
(5-6)
◽
pp. 626-636
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2010 ◽
Vol 36
(14)
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pp. 1148-1156
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1999 ◽
Vol 103
(33)
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pp. 6998-7014
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2019 ◽
Vol 59
(11)
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pp. 4855-4867
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