메뉴 건너뛰기




Volumn 29, Issue SUPPL. 1, 1997, Pages 50-58

Evaluation of comparative protein structure modeling by MODELLER-3

Author keywords

Comparative protein modeling; Evaluation; Modeller

Indexed keywords

DIHYDROFOLATE REDUCTASE; PHOSPHOTRANSFERASE; PROTEIN; PROTEIN UBC 9; UNCLASSIFIED DRUG; LIGASE; UBIQUITIN CONJUGATING ENZYME; UBIQUITIN CONJUGATING ENZYME UBC9; UBIQUITIN-CONJUGATING ENZYME UBC9;

EID: 0031307019     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(1997)1+<50::AID-PROT8>3.0.CO;2-S     Document Type: Article
Times cited : (230)

References (32)
  • 1
    • 0018392721 scopus 로고
    • Comparison of the predicted model of ff-lytic protease with the x-ray structure
    • Delbaere, L.T.J., Brayer, G.D., James, M.N.G. Comparison of the predicted model of ff-lytic protease with the x-ray structure. Nature 279:165-168, 1979.
    • (1979) Nature , vol.279 , pp. 165-168
    • Delbaere, L.T.J.1    Brayer, G.D.2    James, M.N.G.3
  • 3
    • 0030627901 scopus 로고    scopus 로고
    • Protein structures sustain evolutionary drift
    • Rost, B. Protein structures sustain evolutionary drift. Folding Design 2:S19-S24, 1997.
    • (1997) Folding Design , vol.2
    • Rost, B.1
  • 4
    • 0028051828 scopus 로고
    • Derivation of rules for comparative protein modeling from a database of protein structure alignments
    • Šali, A. and Overington, J. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci. 3:1582-1596, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 1582-1596
    • Šali, A.1    Overington, J.2
  • 5
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Šali, A., Blundell, T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815, 1993.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Šali, A.1    Blundell, T.L.2
  • 8
    • 0030908273 scopus 로고    scopus 로고
    • Advances in comparative protein-structure modeling
    • Sánchez, R., Šali, A. Advances in comparative protein-structure modeling. Curr. Opin. Str. Biol. 7:206-214, 1997.
    • (1997) Curr. Opin. Str. Biol. , vol.7 , pp. 206-214
    • Sánchez, R.1    Šali, A.2
  • 10
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S.B., Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453, 1970.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 12
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R.A., McArthur, M.W., Moss, D.S., Thornton, J.M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291, 1993.
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    McArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 14
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • Sippl, M.J. Recognition of errors in three-dimensional structures of proteins. Proteins 17:355-362, 1993.
    • (1993) Proteins , vol.17 , pp. 355-362
    • Sippl, M.J.1
  • 15
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic level
    • Melo, F., Feytmans, E. Novel knowledge-based mean force potential at atomic level. J. Mol. Biol. 267:207-222, 1997.
    • (1997) J. Mol. Biol. , vol.267 , pp. 207-222
    • Melo, F.1    Feytmans, E.2
  • 16
    • 0028343413 scopus 로고
    • Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
    • Koehl, P., Delarue, M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239: 249-275, 1994.
    • (1994) J. Mol. Biol. , vol.239 , pp. 249-275
    • Koehl, P.1    Delarue, M.2
  • 17
    • 0028223845 scopus 로고
    • Predicting protein mutant energetics by self consistent ensemble optimisation
    • Lee, C. Predicting protein mutant energetics by self consistent ensemble optimisation. J. Mol. Biol. 236:918-939, 1994.
    • (1994) J. Mol. Biol. , vol.236 , pp. 918-939
    • Lee, C.1
  • 18
    • 0030623575 scopus 로고    scopus 로고
    • All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of side chains by dead-end elimination
    • Maeyer, M.D., Desmet, J., Lasters, I. All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of side chains by dead-end elimination. Folding Design 2:53-66, 1997.
    • (1997) Folding Design , vol.2 , pp. 53-66
    • Maeyer, M.D.1    Desmet, J.2    Lasters, I.3
  • 19
    • 0009130599 scopus 로고    scopus 로고
    • A structural explanation for the twilight zone of protein sequence homology
    • Chung, S.Y., Subbiah, S. A structural explanation for the twilight zone of protein sequence homology. Structure 4:1123-1127, 1996.
    • (1996) Structure , vol.4 , pp. 1123-1127
    • Chung, S.Y.1    Subbiah, S.2
  • 20
    • 0000179199 scopus 로고
    • Knowledge based modeling of homologous proteins, Part II: Rules for the conformation of substituted side-chains
    • Sutcliffe, M.J., Hayes, F.R.F., Blundell, T.L. Knowledge based modeling of homologous proteins, Part II: Rules for the conformation of substituted side-chains. Protein Eng. 1:385-392, 1987.
    • (1987) Protein Eng. , vol.1 , pp. 385-392
    • Sutcliffe, M.J.1    Hayes, F.R.F.2    Blundell, T.L.3
  • 21
    • 0024816521 scopus 로고
    • Construction of side-chains in homology modelling: Application to the C-terminal lobe of rhizopuspepsin
    • Summers, N.L., Karplus, M. Construction of side-chains in homology modelling: Application to the C-terminal lobe of rhizopuspepsin. J. Mol. Biol. 210:785-811, 1989.
    • (1989) J. Mol. Biol. , vol.210 , pp. 785-811
    • Summers, N.L.1    Karplus, M.2
  • 22
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
    • Bower, M.J., Cohen, F.E., Dunbrack, R.L. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. J. Mol. Biol. 267:1268-1282, 1997.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack, R.L.3
  • 23
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa, S., Jernigan, R.L. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552, 1985.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 24
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl, M.J. Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213:859-883, 1990.
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 25
    • 0029844461 scopus 로고    scopus 로고
    • Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise nonbonded interactions
    • DeBolt, S.E., Skolnick, J. Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise nonbonded interactions. Protein Eng. 9:937-955, 1996.
    • (1996) Protein Eng. , vol.9 , pp. 937-955
    • DeBolt, S.E.1    Skolnick, J.2
  • 26
    • 0027291015 scopus 로고
    • Prediction of protein structure at better than 70% accuracy
    • Rost, B., Sander, C. Prediction of protein structure at better than 70% accuracy. J. Mol. Biol. 232:584-599, 1993.
    • (1993) J. Mol. Biol. , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 27
    • 0023718983 scopus 로고
    • Secondary structure prediction: Combination of three different methods
    • Biou, V., Gibrat, J.-F., Levin, J., Gamier, J. Secondary structure prediction: Combination of three different methods. Protein Eng. 2:185-191, 1988.
    • (1988) Protein Eng. , vol.2 , pp. 185-191
    • Biou, V.1    Gibrat, J.-F.2    Levin, J.3    Gamier, J.4
  • 28
    • 0029872773 scopus 로고    scopus 로고
    • The importance of larger data sets for protein secondary structure prediction with neural networks
    • Chandonia, J.M., Karplus, M. The importance of larger data sets for protein secondary structure prediction with neural networks. Protein Sci. 5:768-774, 1996.
    • (1996) Protein Sci. , vol.5 , pp. 768-774
    • Chandonia, J.M.1    Karplus, M.2
  • 29
    • 0030666224 scopus 로고    scopus 로고
    • Crystal structure of the δ′ subunit of the clamp-loader complex of E. coli DNA polymerase III
    • Guenther, B., Onrust, R., Šali, A., O'Donnell, M., Kuriyan, J. Crystal structure of the δ′ subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91:335-345, 1997.
    • (1997) Cell , vol.91 , pp. 335-345
    • Guenther, B.1    Onrust, R.2    Šali, A.3    O'Donnell, M.4    Kuriyan, J.5
  • 30
    • 0028991962 scopus 로고
    • Modelling mutations and homologous proteins
    • Šali, A. Modelling mutations and homologous proteins. Curr. Opin. Biotech. 6:437-451, 1995.
    • (1995) Curr. Opin. Biotech. , vol.6 , pp. 437-451
    • Šali, A.1
  • 31
    • 0029361476 scopus 로고
    • Protein modeling by satisfaction of spatial restraints
    • Šali, A. Protein modeling by satisfaction of spatial restraints. Mol. Med. Today 1:270-277, 1995.
    • (1995) Mol. Med. Today , vol.1 , pp. 270-277
    • Šali, A.1
  • 32
    • 0009522328 scopus 로고    scopus 로고
    • Comparative protein modeling as an optimization problem
    • Sánchez, R., Šali, A. Comparative protein modeling as an optimization problem. J. Mol. Struct. (Theochem) 398:489-496, 1997.
    • (1997) J. Mol. Struct. (Theochem) , vol.398 , pp. 489-496
    • Sánchez, R.1    Šali, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.