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Cited by 10,830

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

Open access
Maier, James A., Martinez, Carmenza, Kasavajhala, Koushik, Wickstrom, Lauren, Hauser, Kevin E., Simmerling, Carlos·2015·Journal of Chemical Theory and Computation
DOI 10.1021/acs.jctc.5b00255
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Abstract

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.

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Items 101–115 of 115

Metadata

Authors
Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C.
Venue
Journal of Chemical Theory and Computation
Publisher
American Chemical Society (ACS)
Published
2015-07-23
Volume
11
Issue
8
Pages
3696-3713
ISSN
  • 1549-9618 (ISSN-L)
  • 1549-9626
DOI
10.1021/acs.jctc.5b00255
OpenAlex
W2404280981
Cited by
10,830
References
3
FWCI
120.03
Type
journal article
Language
en
Open access
green
Funders
National Institute of General Medical Sciences (GM061678, GM107104)

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