DOI: 10.1021/ja003164o. An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis

An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis

10.1021/ja003164o

Crossref journal-article

American Chemical Society (ACS)

Journal of the American Chemical Society (316)

Bibliography

Wang, W., Lim, W. A., Jakalian, A., Wang, J., Wang, J., Luo, R., Bayly, C. I., & Kollman, P. A. (2001). An Analysis of the Interactions between the Semâ5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis. Journal of the American Chemical Society, 123(17), 3986â3994.

Authors 8

Wei Wang (first)
Wendell A. Lim (additional)
Araz Jakalian (additional)
Jian Wang (additional)
Junmei Wang (additional)
Ray Luo (additional)
Christopher I. Bayly (additional)
Peter A. Kollman (additional)

References 32 Referenced 116

10.1021/cr00023a004 / Chem. Rev. by Kollman P. (1993)
10.1146/annurev.bb.18.060189.002243 / Annu. Rev. Biophys. Biophys. Chem. by Beveridge D. L. (1989)
{'key': 'ja003164ob00003/ja003164ob00003_1', 'first-page': '59', 'volume-title': 'Computer Simulation of Biomolecular Systems', 'author': 'van Gunsteren W.', 'year': '1989'} / Computer Simulation of Biomolecular Systems by van Gunsteren W. (1989)
{'key': 'ja003164ob00004/ja003164ob00004_1', 'first-page': '9409', 'volume': '120', 'author': 'Srinivasan J.', 'year': '1998', 'journal-title': 'J. Am. Chem. Soc.'} / J. Am. Chem. Soc. by Srinivasan J. (1998)
10.1021/ja990935j / J. Am. Chem. Soc. by Massova I. (1999)
10.1021/ja00124a002 / J. Am. Chem. Soc. by Cornell W. D. (1995)
{'key': 'ja003164ob00007/ja003164ob00007_1', 'first-page': '290', 'volume': '4', 'author': 'Case D. A.', 'year': '1994', 'journal-title': 'Curr. Opin. Struct. Biol.'} / Curr. Opin. Struct. Biol. by Case D. A. (1994)
{'key': 'ja003164ob00008/ja003164ob00008_1', 'first-page': '248', 'volume': '80', 'author': 'Cohen G. B.', 'year': '1995', 'journal-title': 'Cell'} / Cell by Cohen G. B. (1995)
10.1146/annurev.biophys.26.1.259 / Annu. Rev. Biophys. Biomol. Struct. by Kuriyan J. (1997)
10.1126/science.278.5346.2075 / Science by Pawson T. (1997)
10.1038/356340a0 / Nature by Clark S. G. (1992)
10.1016/0092-8674(93)90169-Q / Cell by Simon M. A. (1993)
10.1016/0092-8674(93)90170-U / Cell by Olivier J. P. (1993)
{'key': 'ja003164ob00014/ja003164ob00014_1', 'first-page': '1266', 'volume': '3', 'author': 'Lim W. A.', 'year': '1994', 'journal-title': 'Protein Sci.'} / Protein Sci. by Lim W. A. (1994)
10.1126/science.282.5396.2088 / Science by Nguyen J. T. (1998)
10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P / J. Comput. Chem. by Jakalian A. (2000)
{'key': 'ja003164ob00017/ja003164ob00017_1', 'volume-title': 'Manuscript in preparation', 'author': 'Jakalian A.', 'year': '2000'} / Manuscript in preparation by Jakalian A. (2000)
{'key': 'ja003164ob00018/ja003164ob00018_1', 'first-page': '225', 'volume': '1', 'author': 'Lim W. A.', 'year': '1994', 'journal-title': 'Nat. Struct. Biol.'} / Nat. Struct. Biol. by Lim W. A. (1994)
10.1016/0010-4655(95)00041-D / Comput. Phys. Commun. by Pearlman D. A. (1995)
10.1063/1.445869 / J. Chem. Phys. by Jorgensen W. L. (1983)
10.1016/0263-7855(88)80054-7 / J. Mol. Graphics by Ferrin T. E. (1988)
10.1063/1.464397 / J. Chem. Phys. by Darden T. A. (1993)
{'key': 'ja003164ob00023/ja003164ob00023_1', 'first-page': '341', 'volume': '23', 'author': 'Rychaert J. P.', 'year': '1977', 'journal-title': 'J. Comput. Phys.'} / J. Comput. Phys. by Rychaert J. P. (1977)
10.1021/ar000033j / Acc. Chem. Res. by Kollman P. A. (2000)
{'key': 'ja003164ob00025/ja003164ob00025_1', 'first-page': '335', 'volume': '9', 'author': 'Gilson M. K.', 'year': '1987', 'journal-title': 'J. Comput. Chem.'} / J. Comput. Chem. by Gilson M. K. (1987)
10.1006/jmbi.2000.4057 / J. Mol. Bol. by Wang W. (2000)
10.1021/j100058a043 / J. Phys. Chem. by Sitkoff D. (1994)
10.1021/j100142a004 / J. Phys. Chem. by Bayly C. I. (1993)
10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y / Biopolymers by Sanner M. F. (1996)
10.1093/nar/25.17.3389 / J. Nucleic Acids Res. by Altschul S. F. (1997)
10.1006/jmbi.1997.1620 / J. Mol. Biol. by Ptitsyn O. B. (1998)
10.1006/jmbi.1999.2920 / J. Mol. Biol. by Ptitsyn O. B. (1999)

Dates

Type	When
Created	23 years ago (July 26, 2002, 12:56 a.m.)
Deposited	3 years, 11 months ago (Sept. 21, 2021, 10:31 a.m.)
Indexed	1 month ago (July 20, 2025, 6:55 p.m.)
Issued	24 years, 4 months ago (April 5, 2001)
Published	24 years, 4 months ago (April 5, 2001)
Published Online	24 years, 4 months ago (April 5, 2001)
Published Print	24 years, 3 months ago (May 1, 2001)

Funders 0

None

BibTeX

@article{Wang_2001, title={An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis}, volume={123}, ISSN={1520-5126}, url={http://dx.doi.org/10.1021/ja003164o}, DOI={10.1021/ja003164o}, number={17}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Wang, Wei and Lim, Wendell A. and Jakalian, Araz and Wang, Jian and Wang, Junmei and Luo, Ray and Bayly, Christopher I. and Kollman, Peter A.}, year={2001}, month=apr, pages={3986–3994} }

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    {
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      "first-page": "492",
      "DOI": "10.1146/annurev.bb.18.060189.002243",
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      "author": "Beveridge D. L.",
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      "journal-title": "Annu. Rev. Biophys. Biophys. Chem."
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    {
      "key": "ja003164ob00003/ja003164ob00003_1",
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      "volume-title": "Computer Simulation of Biomolecular Systems",
      "author": "van Gunsteren W.",
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    {
      "key": "ja003164ob00004/ja003164ob00004_1",
      "first-page": "9409",
      "volume": "120",
      "author": "Srinivasan J.",
      "year": "1998",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "ja003164ob00005/ja003164ob00005_1",
      "doi-asserted-by": "crossref",
      "first-page": "8143",
      "DOI": "10.1021/ja990935j",
      "volume": "121",
      "author": "Massova I.",
      "year": "1999",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "ja003164ob00006/ja003164ob00006_1",
      "doi-asserted-by": "crossref",
      "first-page": "5197",
      "DOI": "10.1021/ja00124a002",
      "volume": "117",
      "author": "Cornell W. D.",
      "year": "1995",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "ja003164ob00007/ja003164ob00007_1",
      "first-page": "290",
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      "key": "ja003164ob00011/ja003164ob00011_1",
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      "DOI": "10.1063/1.445869",
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      "author": "Jorgensen W. L.",
      "year": "1983",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "ja003164ob00021/ja003164ob00021_1",
      "doi-asserted-by": "crossref",
      "first-page": "27",
      "DOI": "10.1016/0263-7855(88)80054-7",
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      "author": "Ferrin T. E.",
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    },
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      "key": "ja003164ob00022/ja003164ob00022_1",
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    },
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      "key": "ja003164ob00023/ja003164ob00023_1",
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      "first-page": "582",
      "DOI": "10.1006/jmbi.2000.4057",
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