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Volumn 15, Issue 4, 1999, Pages 327-332

Automated analysis of interatomic contacts in proteins

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 13044272912     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.4.327     Document Type: Article
Times cited : (741)

References (20)
  • 1
    • 0030847766 scopus 로고    scopus 로고
    • Protein Data Bank archives of three-dimensional macromolecular structures
    • Abola, E.E., Sussman, J.L., Prilusky, J. and Manning, N.O. (1997) Protein Data Bank archives of three-dimensional macromolecular structures. Methods Enzymol., 277, 556-571.
    • (1997) Methods Enzymol. , vol.277 , pp. 556-571
    • Abola, E.E.1    Sussman, J.L.2    Prilusky, J.3    Manning, N.O.4
  • 3
    • 0030957127 scopus 로고    scopus 로고
    • The role of long-range interactions in defining the secondary structure of proteins is overestimated
    • Fiser, A., Dosztanyi, Z. and Simon, I. (1997) The role of long-range interactions in defining the secondary structure of proteins is overestimated. Comput. Applic. Biosci., 13, 297-301.
    • (1997) Comput. Applic. Biosci. , vol.13 , pp. 297-301
    • Fiser, A.1    Dosztanyi, Z.2    Simon, I.3
  • 4
    • 0015222647 scopus 로고
    • The interpretation of protein structure: Estimation of static accessibility
    • Lee, B. and Richards, F.M. (1971) The interpretation of protein structure: Estimation of static accessibility. J. Mol. Biol., 55, 379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 5
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 6
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng, E.C., Shoichet, B.K. and Kuntz, I.D. (1992) Automated docking with grid-based energy evaluation. J. Comput. Chem., 13, 505-524.
    • (1992) J. Comput. Chem. , vol.13 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 7
    • 0030730580 scopus 로고    scopus 로고
    • Non-randomness in side-chain packing: The distribution of interplanar angles
    • Mitchell, J.B.O., Laskowski, R.A. and Thornton, J.M. (1997) Non-randomness in side-chain packing: the distribution of interplanar angles. Proteins, 29, 370-380.
    • (1997) Proteins , vol.29 , pp. 370-380
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Thornton, J.M.3
  • 8
    • 0027191901 scopus 로고
    • A new substitution matrix for protein sequence searches based on contact frequencies in protein structures
    • Miyazawa, S. and Jernigan, R.L. (1993) A new substitution matrix for protein sequence searches based on contact frequencies in protein structures. Protein Eng., 6, 267-278.
    • (1993) Protein Eng. , vol.6 , pp. 267-278
    • Miyazawa, S.1    Jernigan, R.L.2
  • 9
    • 0028167665 scopus 로고
    • X-ray crystallographic study of pyroxal 5-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form
    • Okamoto, A., Higuchi, T., Hirotsu, K., Kuramitsu, S. and Kagamiyama, H. (1994) X-ray crystallographic study of pyroxal 5-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form. J. Biochem. (Japan), 116, 95-107.
    • (1994) J. Biochem. (Japan) , vol.116 , pp. 95-107
    • Okamoto, A.1    Higuchi, T.2    Hirotsu, K.3    Kuramitsu, S.4    Kagamiyama, H.5
  • 10
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M., Kramer, B., Lengauer, T. and Klebe, G. (1996) A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol., 261, 470-489.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 11
    • 0028081403 scopus 로고
    • Structural features can be unconservated in proteins with similar folds
    • Russell, R.B. and Barton, G.J. (1994) Structural features can be unconservated in proteins with similar folds. J. Mol. Biol., 244, 332-350.
    • (1994) J. Mol. Biol. , vol.244 , pp. 332-350
    • Russell, R.B.1    Barton, G.J.2
  • 12
    • 0032080921 scopus 로고    scopus 로고
    • Relationships between protein sequence and structure patterns based on residue contacts
    • Selbig, J. and Argos, P. (1998) Relationships between protein sequence and structure patterns based on residue contacts. Proteins, 31, 172-185.
    • (1998) Proteins , vol.31 , pp. 172-185
    • Selbig, J.1    Argos, P.2
  • 13
    • 0028915315 scopus 로고
    • Modeling the quinone-B binding site of the photosystem-II reaction center using notions of complementarity and contact-surface between atoms
    • Sobolev, V. and Edelman, M. (1995) Modeling the quinone-B binding site of the photosystem-II reaction center using notions of complementarity and contact-surface between atoms. Proteins, 21, 214-225.
    • (1995) Proteins , vol.21 , pp. 214-225
    • Sobolev, V.1    Edelman, M.2
  • 14
    • 0029937340 scopus 로고    scopus 로고
    • Molecular docking using surface complementarity
    • Sobolev, V., Wade, R.C., Vriend, G. and Edelman, M. (1996) Molecular docking using surface complementarity. Proteins, 25, 120-129.
    • (1996) Proteins , vol.25 , pp. 120-129
    • Sobolev, V.1    Wade, R.C.2    Vriend, G.3    Edelman, M.4
  • 15
    • 0031296899 scopus 로고    scopus 로고
    • CASP2 molecular docking predictions with the LIGIN software
    • Sobolev, V., Moallem, T.M., Wade, R.C., Vriend, G. and Edelman, M. (1997) CASP2 molecular docking predictions with the LIGIN software. Proteins, 1(Suppl.), 210-214.
    • (1997) Proteins , vol.1 , Issue.SUPPL. , pp. 210-214
    • Sobolev, V.1    Moallem, T.M.2    Wade, R.C.3    Vriend, G.4    Edelman, M.5
  • 16
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still, W.C., Tempczyk, A., Hawley, R.C. and Hendrickson, J. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc., 112, 6127-6131.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6131
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, J.4
  • 17
    • 0028907319 scopus 로고
    • A procedure for the automatic determination of hydrophobic cores in protein structures
    • Swindells, M.B. (1995) A procedure for the automatic determination of hydrophobic cores in protein structures. Protein Sci., 4, 93-102.
    • (1995) Protein Sci. , vol.4 , pp. 93-102
    • Swindells, M.B.1
  • 18
    • 0030158429 scopus 로고    scopus 로고
    • PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
    • Van Aalten, D.M., Bywater, R., Findlay, J.B., Hendlich, M., Hooft, R.W. and Vriend, G. (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Design, 10, 255-262.
    • (1996) J. Comput. Aided Mol. Design , vol.10 , pp. 255-262
    • Van Aalten, D.M.1    Bywater, R.2    Findlay, J.B.3    Hendlich, M.4    Hooft, R.W.5    Vriend, G.6
  • 19
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • Vriend, G. (1990) WHAT IF: A molecular modeling and drug design program. J. Mol. Graph., 8, 52-56.
    • (1990) J. Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 20
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace, A.C., Laskowski, R.A. and Thornton, J.M. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 8, 127-134.
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.