메뉴 건너뛰기




Volumn 135, Issue 6, 2011, Pages

Energy design for protein-protein interactions

Author keywords

[No Author keywords available]

Indexed keywords

CELL FUNCTIONS; DOCKING PROBLEMS; EMPIRICAL DATA; ENERGY DESIGN; ENERGY FUNCTIONS; ENERGY MINIMA; ENZYMATIC REACTION; FAST FOURIER TRANSFORM ALGORITHM; INDEPENDENT SET; LEARNING PARAMETERS; NEGATIVE EXAMPLES; OPTIMAL ENERGY; PROTEIN COMPLEXES; PROTEIN-PROTEIN INTERACTIONS; SCORING FUNCTIONS;

EID: 80051880753     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3615722     Document Type: Article
Times cited : (14)

References (53)
  • 1
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: Preparing the next generation of molecular biologists
    • DOI 10.1016/S0092-8674(00)80922-8
    • B. Alberts, Cell 92, 291 (1998). 10.1016/S0092-8674(00)80922-8 (Pubitemid 28093007)
    • (1998) Cell , vol.92 , Issue.3 , pp. 291-294
    • Alberts, B.1
  • 4
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • DOI 10.1002/prot.20033
    • A. Onufriev, D. Bashford, and D. A. Case, Proteins: Struct., Funct., Bioinf. 55 (2), 383 (2004). 10.1002/prot.20033 (Pubitemid 38437495)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.2 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 6
    • 47349110113 scopus 로고    scopus 로고
    • A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins
    • DOI 10.1002/prot.21976
    • B. K. Vallat, J. Pillardy, and R. Elber, Proteins: Struct., Funct., Bioinf. 72 (3), 910 (2008). 10.1002/prot.21976 (Pubitemid 352000869)
    • (2008) Proteins: Structure, Function and Genetics , vol.72 , Issue.3 , pp. 910-928
    • Vallat, B.K.1    Pillardy, J.2    Elber, R.3
  • 9
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • DOI 10.1002/prot.1087
    • H. Lu and J. Skolnick, Proteins: Struct., Funct., Bioinf. 44 (3), 223 (2001). 10.1002/prot.1087 (Pubitemid 32702231)
    • (2001) Proteins: Structure, Function and Genetics , vol.44 , Issue.3 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 14
    • 0034308163 scopus 로고    scopus 로고
    • 10.1002/109 7-0134(20001 001)41:140::AID-PRO T703.0.CO;2-U
    • D. Tobi and R. Elber, Proteins: Struct., Funct., Genet. 41 (1), 40 (2000). 10.1002/1097-0134(20001001)41:140::AID-PROT703.0.CO;2-U
    • (2000) Proteins: Struct., Funct., Genet. , vol.41 , Issue.1 , pp. 40
    • Tobi, D.1    Elber, R.2
  • 20
  • 22
    • 24344479166 scopus 로고    scopus 로고
    • Atomically detailed potentials to recognize native and approximate protein structures
    • DOI 10.1002/prot.20585
    • J. Qiu and R. Elber, Proteins: Struct., Funct., Bioinf. 61 (1), 44 (2005). 10.1002/prot.20585 (Pubitemid 41262916)
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.1 , pp. 44-55
    • Qiu, J.1    Elber, R.2
  • 24
    • 33644848651 scopus 로고    scopus 로고
    • Optimal design of protein docking potentials: Efficiency and limitations
    • DOI 10.1002/prot.20859
    • D. Tobi and I. Bahar, Proteins: Struct., Funct., Bioinf. 62 (4), 970 (2006). 10.1002/prot.20859 (Pubitemid 43364161)
    • (2006) Proteins: Structure, Function and Genetics , vol.62 , Issue.4 , pp. 970-981
    • Tobi, D.1    Bahar, I.2
  • 27
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • DOI 10.1006/jmbi.1997.1203
    • H. A. Gabb, R. M. Jackson, and M. J. E. Sternberg, J. Mol. Biol. 272 (1), 106 (1997). 10.1006/jmbi.1997.1203 (Pubitemid 27395541)
    • (1997) Journal of Molecular Biology , vol.272 , Issue.1 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 31
    • 0037340493 scopus 로고    scopus 로고
    • 10.1016/S0006-3495(03)74997-2
    • H. Lu, L. Lu, and J. Skolnick, Biophys. J. 84, 1895 (2003). 10.1016/S0006-3495(03)74997-2
    • (2003) Biophys. J. , vol.84 , pp. 1895
    • Lu, H.1    Lu, L.2    Skolnick, J.3
  • 32
    • 34248513078 scopus 로고    scopus 로고
    • ZRANK: Reranking protein docking predictions with an optimized energy function
    • DOI 10.1002/prot.21373
    • B. Pierce and Z. Weng, Proteins: Struct., Funct., Bioinf. 67 (4), 1078 (2007). 10.1002/prot.21373 (Pubitemid 46753952)
    • (2007) Proteins: Structure, Function and Genetics , vol.67 , Issue.4 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 33
    • 0345832301 scopus 로고    scopus 로고
    • ClusPro: An automated docking and discrimination method for the prediction of protein complexes
    • DOI 10.1093/bioinformatics/btg371
    • S. R. Comeau, D. W. Gatchell, S. Vajda, and C. J. Camacho, Bioinformatics 20 (1), 45 (2004). 10.1093/bioinformatics/btg371 (Pubitemid 38088339)
    • (2004) Bioinformatics , vol.20 , Issue.1 , pp. 45-50
    • Comeau, S.R.1    Gatchell, D.W.2    Vajda, S.3    Camacho, C.J.4
  • 34
    • 33747840389 scopus 로고    scopus 로고
    • GRAMM-X public web server for protein-protein docking
    • DOI 10.1093/nar/gkl206
    • A. Tovchigrechko and I. A. Vakser, Nucleic Acids Res. 34 (suppl. 2), W310 (2006). 10.1093/nar/gkl206 (Pubitemid 44529784)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISSUE
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 35
    • 0031552370 scopus 로고    scopus 로고
    • Determination of atomic desolvation energies from the structures of crystallized proteins
    • DOI 10.1006/jmbi.1996.0859
    • C. Zhang, G. Vasmatzis, J. L. Cornette, and C. DeLisi, J. Mol. Biol. 267 (3), 707 (1997). 10.1006/jmbi.1996.0859 (Pubitemid 27170692)
    • (1997) Journal of Molecular Biology , vol.267 , Issue.3 , pp. 707-726
    • Zhang, C.1    Vasmatzis, G.2    Cornette, J.L.3    DeLisi, C.4
  • 39
    • 46449084711 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function for protein-protein recognition
    • DOI 10.1002/prot.21949
    • S. Y. Huang and X. Zou, Proteins: Struct., Funct., Bioinf. 72 (2), 557 (2008). 10.1002/prot.21949 (Pubitemid 351928512)
    • (2008) Proteins: Structure, Function and Genetics , vol.72 , Issue.2 , pp. 557-579
    • Huang, S.-Y.1    Zou, X.2
  • 44
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • DOI 10.1093/nar/gki524
    • Y. Zhang and J. Skolnick, Nucleic Acids Res. 33 (7), 2302 (2005). 10.1093/nar/gki524 (Pubitemid 41439897)
    • (2005) Nucleic Acids Research , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 46
    • 0032960853 scopus 로고    scopus 로고
    • 10.1002/(SIC I)1097-0134(199 90101)34:149::AID-PR OT53.0.CO;2-L
    • S. Miyazawa and R. L. Jernigan, Proteins: Struct., Funct., Bioinf. 34 (1), 49 (1999). 10.1002/(SICI)1097-0134(19990101)34:149::AID-PROT53.0.CO;2-L
    • (1999) Proteins: Struct., Funct., Bioinf. , vol.34 , Issue.1 , pp. 49
    • Miyazawa, S.1    Jernigan, R.L.2
  • 47
    • 0026785519 scopus 로고
    • 10.1016/0022-2836(92)90228-C
    • V. N. Maiorov and G. M. Crippen, J. Mol. Biol. 227 (3), 876 (1992). 10.1016/0022-2836(92)90228-C
    • (1992) J. Mol. Biol. , vol.227 , Issue.3 , pp. 876
    • Maiorov, V.N.1    Crippen, G.M.2
  • 48
    • 0000171351 scopus 로고    scopus 로고
    • Pairwise contact potentials are unsuitable for protein folding
    • DOI 10.1063/1.477748, PII S0021960698502474
    • M. Vendruscolo and E. Domany, J. Chem. Phys. 109 (24), 11101 (1998). 10.1063/1.477748 (Pubitemid 128675160)
    • (1998) Journal of Chemical Physics , vol.109 , Issue.24 , pp. 11101-11108
    • Vendruscolo, M.1    Domany, E.2
  • 50
    • 27844505722 scopus 로고    scopus 로고
    • Advances in protein structure prediction and de novo protein design: A review
    • DOI 10.1016/j.ces.2005.04.009, PII S0009250905002988, Biomolecular Engineering
    • C. A. Floudas, H. K. Fung, S. R. McAllister, M. Monnigmann, and R. Rajgaria, Chem. Eng. Sci. 61 (3), 966 (2006). 10.1016/j.ces.2005.04.009 (Pubitemid 41655853)
    • (2006) Chemical Engineering Science , vol.61 , Issue.3 , pp. 966-988
    • Floudas, C.A.1    Fung, H.K.2    McAllister, S.R.3    Monnigmann, M.4    Rajgaria, R.5
  • 51
    • 10244245448 scopus 로고    scopus 로고
    • Developing optimal non-linear scoring function for protein design
    • DOI 10.1093/bioinformatics/bth369
    • C. Hu, X. Li, and J. Liang, Bioinformatics 20 (17), 3080 (2004). 10.1093/bioinformatics/bth369 (Pubitemid 39619199)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3080-3098
    • Hu, C.1    Li, X.2    Liang, J.3
  • 52
    • 0028713181 scopus 로고
    • 10.1007/BF01582228
    • F. A. Potra, Math. Program. 67 (1), 383 (1994). 10.1007/BF01582228
    • (1994) Math. Program. , vol.67 , Issue.1 , pp. 383
    • Potra, F.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.