Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 14,311

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D., Karplus, M.·1998·The Journal of Physical Chemistry B
DOI 10.1021/jp973084f
Open this paper in CoChat — free account

Abstract

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1021/jp973084f

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 1 references

Research works printed but not linked: 114

  1. Brooks, C. L. , III; Karplus, M. ; Pettitt, B. M. Proteins, A Theoretical Perspective Dynamics, Structure, and Thermodynamics ; John Wiley and Sons: New York, 1988; Vol. LXXI.
  2. McCammon, J. A. ; Harvey, S. Dynamics of Proteins and Nucleic Acids ; Cambridge University Press: 1987. · DOI · Paper page
  3. 10.1002/jcc.540040211 · DOI · Paper page
  4. Reiher, W. E. , III. Ph.D. Thesis, Harvard University, 1985.
  5. 10.1021/ja00333a021 · DOI
  6. 10.1002/jcc.540070216 · DOI · Paper page
  7. 10.1021/ja00214a001 · DOI
  8. (a)Feng, M.H. ; Philippopoulos, M. ; MacKerell, A. D., Jr. ; Lim, C. J. Am. Chem. Soc. 1996 , 118 , 11265. (b)Schmidt, J. M. ; Brüschweiler, R. Ernst, R. R. ; Dunbrack, R. L., Jr. ; Joseph, D. ; Karplus, M. J. Am. Chem. Soc . 1993 , 115 , 8747−8756. · DOI
  9. 10.1002/jcc.540120208 · DOI
  10. 10.1021/j100389a010 · DOI
  11. 10.1021/ja00153a017 · DOI · Paper page
  12. Schlenkrich, M. ; Brickmann, J. ; MacKerell, A. D., Jr. ; Karplus, M. Biological Membranes: A Molecular Perspective from Computation and Experiment ; Birkäuser: Boston, MA, 1996; p 31. · DOI
  13. 10.1063/1.472061 · DOI
  14. (a)Jorgensen, W. L. J. Am. Chem. Soc. 1990 , 112 , 4768. (b) Burley, S. K.Petsko, G. A. Adv. Protein Chem. 1988 , 39 , 125.
  15. The CHARMM program can be obtained by not-for-profit institutions under a license agreement by writing to the CHARMM Development Program, Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138 (email: marci@tammy.harvard.edu).
  16. 10.1021/ja00291a014 · DOI
  17. 10.1063/1.445869 · DOI · Paper page
  18. Smith, J. C. ; Karplus, M. J. Am. Chem. Soc. 1992 , 114 , 801. · DOI
  19. 10.1107/S0567740879009249 · DOI
  20. 10.1021/j100065a023 · DOI
  21. 10.1038/nsb0594-334 · DOI · Paper page
  22. 10.1002/jcc.540110514 · DOI
  23. Berendsen, H. J. C. ; Grigera, J. R. ; Straatsma, J. Phys. Chem. 1987 , 91 , 6269. · DOI · Paper page
  24. 10.1016/0022-2852(74)90261-6 · DOI
  25. 10.1021/ja00008a002 · DOI · Paper page
  26. Halgren, T. A. J. Comput. Chem. 1996 , 17 , 520. · DOI
  27. 10.1021/j100179a013 · DOI
  28. 10.1126/science.1411573 · DOI
  29. Moet-Ner, M. J. Am. Chem. Soc. 1988 , 110 , 3858. · DOI
  30. Moet-Ner, M. J. Am. Chem. Soc. 1988 , 110 , 3071. · DOI
  31. Moet-Ner, M. J. Am. Chem. Soc. 1988 , 110 , 3075. · DOI
  32. Moet-Ner, M. J. Am. Chem. Soc. 1988 , 110 , 3854. · DOI
  33. Gao, J. Ph.D. Thesis, Department of Chemistry, Purdue University, 1987.
  34. Jorgensen, W. L. J. Phys. Chem. 1986 , 90 , 1276. · DOI
  35. Stote R. H., 1991, J. Chim. Phys., 88, 2419, 10.1051/jcp/1991882419 · DOI
  36. 10.1016/0021-9991(77)90098-5 · DOI · Paper page
  37. Brünger, A. T. ; Karplus, M. Proteins 1988 , 4 , 148. · DOI
  38. Field, M. J. ; Karplus, M. Harvard University, Cambridge, MA. Unpublished results,1992.
  39. Berendsen, H. J. C. ; Postma, J. P. M. ; van Gunsteren, W. F. ; DiNola, A. Haak, J. R. J. Chem. Phys. 1984 , 81 , 3684. · DOI · Paper page
  40. 10.1038/290107a0 · DOI · Paper page
  41. Wlodawer, A. ; Walter, J. ; Huber, R. ; Sjölin, L. J. Mol. Biol. 1984 , 180 , 301. · DOI · Paper page
  42. Kuriyan, J. ; Wilz, S. ; Karplus, M. ; Petsko, G. J. Mol. Biol. 1986 , 192 , 227. · DOI
  43. 10.1073/pnas.88.7.2773 · DOI
  44. 10.1016/0079-6107(84)90007-5 · DOI
  45. Burling, F. T. ; Weis, W. I. ; Flaherty, K. M. ; Brünger, A. T. Science 1996 , 271 , 72. · DOI
  46. 10.1002/bip.360310405 · DOI
  47. 10.1002/bip.360310207 · DOI
  48. 10.1021/ja00484a048 · DOI
  49. 10.1021/ja00715a037 · DOI
  50. Kostansek, E. C. ; Thiessen, W. E. ; Schomburg, D. ; Lipscomb, W. N. J. Am. Chem. Soc. 1979 , 101 , 5811. · DOI
  51. Karle, I. L. J. Am. Chem. Soc. 1978 , 100 , 1286. · DOI
  52. 10.1021/ja00221a012 · DOI
  53. Grant, J. A. ; Williams, R. L. ; Scheraga, H. A. Biopolymers 1990 , 30 , 929. · DOI
  54. 10.1080/07391102.1991.10507872 · DOI
  55. Guo, H. ; Karplus, M. J. Phys. Chem. 1992 , 96 , 7273. · DOI
  56. Guo, H. ; Karplus, M. J. Phys. Chem. 1994 , 98 , 7104. · DOI
  57. Katz, J. ; Post, B. Acta Crystallogr. 1960 , 13 , 624. · DOI
  58. Hamzaoui, F. ; Baert, F. Acta Crystallogr. 1994 , C50 , 757−579. · DOI
  59. Benedetti, E. In Peptides: Proceedings of the 5th American Peptide Symposium ; John Wiley & Sons Inc. New York, 1979; p 257.
  60. Kitano, M. ; Fukuyama, T. ; Kuchitsu, B. Bull. Chem. Soc. Jpn. 1973 , 46 , 384. · DOI
  61. Jorgensen, W. L. ; Gao, J. J. Am. Chem. Soc. 1988 , 110 , 4212. · DOI
  62. 10.1021/ja00114a028 · DOI
  63. 10.1021/ja00105a036 · DOI
  64. Gould, I. R. ; Cornell, W. D. ; Hiller, I. H. J. Am. Chem. Soc. 1994 , 116 , 9250. · DOI
  65. (a)Jones, R. J. Mol. Spectrosc. 1963 , 11 , 411. (b)Fillaux, F. ; DeLoze, C. J. J. Chim. Phys. 1976 , 73 , 1004. · DOI
  66. 10.1002/bip.360260514 · DOI
  67. Sugawara, Y. ; Hirakawa, A. ; Tsuboi, M. ; Kato, S. ; Morokuma, K. J. Mol. Spectrosc. 1986 , 115 , 21. · DOI
  68. (a)Mirkin, N. ; Krimm, S. J. Mol. Struct. 1991 , 242 , 143. (b) Chen, X. G.Schweitzer-Stenner, R. ; Asher, S. A. ; Mirkin, N. G. ; Krimm, S. J. Phys. Chem. 1995 , 99 , 3074. · DOI
  69. Miazawa, T. ; Shimanouchi, T. ; Mizushima, S. J. Chem. Phys. 1958 , 29 , 611. · DOI
  70. Itoh, K. ; Shimanouchi, T. Biopolymers 1967 , 5 , 921. · DOI
  71. 10.1039/c29710001404 · DOI
  72. Cornell, W. D. ; Cieplak, P. ; Bayly, C. I. ; Gould, I. R. ; Merz, K. M., Jr. Ferguson, D. M. ; Spellmeyer, D. C. ; Fox, T. ; Caldwell, J. W. Kollman, P. A. J. Am. Chem. Soc. 1995 , 117 , 5179. · DOI · Paper page
  73. Vásquez, M. ; Némethy, G. ; Scheraga, H. A. Macromolecules 1983 , 16 , 1043. · DOI
  74. 10.1021/ja00019a007 · DOI
  75. 10.1021/ja00039a057 · DOI
  76. Head-Gordon, T. ; Head-Gordon, M. ; Frisch, M. J. ; Brooks, C. , III; Pople, J. Int. J. Quantum Chem. Quantum Biol. Symp. 1989 , 16 , 311.
  77. Head-Gordon, T. ; Head-Gordon, M. ; Frisch, M. J. ; Brooks, C. L. I. Pople, J. A. J. Am. Chem. Soc. 1991 , 113 , 5989. · DOI
  78. Beachy, M. D. ; Chasman, D. ; Murphy, R. B. ; Halgren, T. A. ; Friesner, R. A. J. Am. Chem. Soc. 1997 , 119 , 5908. · DOI
  79. 10.1021/ja00315a051 · DOI · Paper page
  80. Deng, Z. ; Polavarapu, P. L. ; Ford, S. J. ; Hecht, L. ; Barron, L. D. Ewig, C. S. ; Jalkanen, K. J. Phys. Chem. 1996 , 100 , 2025. · DOI
  81. Brooks, C. L. , III; Case, D. A. Chem. Rev. 1993 , 93 , 2487. · DOI
  82. 10.1002/jcc.540160702 · DOI
  83. Gelin, B. ; Karplus, M. J. Am. Chem. Soc. 1975 , 97 , 6996. · DOI
  84. Kang, Y. K. ; No, K. T. ; Scheraga, H. A. J. Phys. Chem. 1996 , 100 , 15588. · DOI
  85. 10.1002/jcc.540160807 · DOI
  86. Halgren, T. A. J. Comput. Chem. 1996 , 17 , 490. · DOI
  87. 10.1016/0166-1280(94)80096-0 · DOI
  88. 10.1080/00268978000101781 · DOI
  89. Riddick. J. A.Bunger, W. B. ; Sakano, T. K. Organic Solvents: Physical Properties and Methods of Purification ; John Wiley & Sons: New York, 1986.
  90. 10.1007/BFb0050146 · DOI
  91. 10.1021/ja00292a007 · DOI
  92. 10.1021/jp9624257 · DOI
  93. 10.1021/ja9621760 · DOI · Paper page
  94. Harada, Y. ; Iitaka, Y. Acta Crystallogr. 1974 , B30 , 1452. · DOI
  95. 10.1006/jmbi.1996.0705 · DOI
  96. Stone, A. J. ; Price, S. L. J. Phys. Chem. 1988 , 92 , 2: 3325. · DOI
  97. Hall, D. ; Pavitt, N. J. Comput. Chem. 1984 , 5 , 441. · DOI
  98. 10.1038/267585a0 · DOI · Paper page
  99. Karplus, M. ; Petsko, G. A. Nature 1990 , 347 , 631. · DOI · Paper page
  100. 10.1073/pnas.80.14.4315 · DOI
  101. 10.1021/bi00539a001 · DOI
  102. 10.1016/0022-2836(88)90389-0 · DOI
  103. 10.1016/S0022-2836(05)80363-8 · DOI
  104. Levy, R. M. ; Sheridan, R. P. ; Keepers, J. W. ; Dubey, G. S. Swaminathan, S. ; Karplus, M. Biophys. J. 1985 , 48 , 509. · DOI
  105. 10.1002/prot.340070407 · DOI
  106. 10.1006/jmbi.1993.1143 · DOI
  107. 10.1016/0022-2836(86)90295-0 · DOI
  108. Elber, R. ; Karplus, M. Science 1987 , 235 , 318. · DOI · Paper page
  109. Phillips, G. N., Jr. Biophys. J. 1990 , 57 , 381. · DOI
  110. 10.1021/ja00283a005 · DOI
  111. Boczko, E. M. ; Brooks, C. L. , III. Science 1995 , 269 , 393. · DOI
  112. Lazaridis, T. ; Karplus, M. Science 1997 , 278 , 1928. · DOI
  113. 10.1073/pnas.91.24.11631 · DOI
  114. 10.1002/(SICI)1096-987X(19970130)18:2%3C221::AID-JCC7%3E3.0.CO;2-X · DOI

Cited by

Items 101–139 of 139

Metadata

Authors
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D., & Karplus, M.
Venue
The Journal of Physical Chemistry B
Publisher
American Chemical Society (ACS)
Published
1998-04-01
Volume
102
Issue
18
Pages
3586-3616
ISSN
  • 1520-5207 (ISSN-L)
  • 1520-6106
DOI
10.1021/jp973084f
OpenAlex
W2027408247
Cited by
14,311
References
1
FWCI
40.52
Type
journal article
Language
en
Open access
closed

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.