메뉴 건너뛰기




Volumn 53, Issue 4, 2006, Pages 533-557

Fast and accurate algorithms for protein side-chain packing

Author keywords

Approximate algorithm; Polynomial time approximation scheme; Protein side chain packing; Tree decomposition

Indexed keywords

POLYNOMIAL-TIME APPROXIMATION SCHEMES (PTAS); PROTEIN SIDE CHAIN PACKING; PROTEIN STRUCTURES; TREE DECOMPOSITION;

EID: 33748944332     PISSN: 00045411     EISSN: 00045411     Source Type: Journal    
DOI: 10.1145/1162349.1162350     Document Type: Article
Times cited : (78)

References (43)
  • 1
    • 14544303007 scopus 로고    scopus 로고
    • NP-hardness results for protein side-chain packing
    • S. Miyano and T. Takagi, Eds.
    • AKUTSU, T. 1997. NP-hardness results for protein side-chain packing. In Genome Informatics 8, S. Miyano and T. Takagi, Eds. 180-186.
    • (1997) Genome Informatics , vol.8 , pp. 180-186
    • Akutsu, T.1
  • 5
    • 0032201716 scopus 로고    scopus 로고
    • An optimal algorithm for approximate nearest neighbor searching in fixed dimensions
    • ARYA, S., MOUNT, D., NETANYAHU, N., SILVERMAN, R., AND WU, A. 1998. An optimal algorithm for approximate nearest neighbor searching in fixed dimensions. J. ACM 45, 891-923.
    • (1998) J. ACM , vol.45 , pp. 891-923
    • Arya, S.1    Mount, D.2    Netanyahu, N.3    Silverman, R.4    Wu, A.5
  • 7
    • 0344392004 scopus 로고    scopus 로고
    • The minimum degree heuristic and the minimal triangulation process
    • Springer-Verlag, New York
    • BERRY, A., HEGGERNES, P., AND SIMONET, G. 2003. The minimum degree heuristic and the minimal triangulation process. In Lecture Notes in Computer Science, vol. 2880. Springer-Verlag, New York, 58-70.
    • (2003) Lecture Notes in Computer Science , vol.2880 , pp. 58-70
    • Berry, A.1    Heggernes, P.2    Simonet, G.3
  • 8
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
    • BOWER, M., COHEN, F., AND DUNBRACK, JR., R. L. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. J. Mol. Biol. 267, 1268-1282.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1268-1282
    • Bower, M.1    Cohen, F.2    Dunbrack Jr., R.L.3
  • 9
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • CANUTESCU, A., SHELENKOV, A., AND DUNBRACK, JR., R. L. 2003. A graph-theory algorithm for rapid protein side-chain prediction. Prot. Sci. 12, 2001-2014.
    • (2003) Prot. Sci. , vol.12 , pp. 2001-2014
    • Canutescu, A.1    Shelenkov, A.2    DUNBRACK Jr., R.L.3
  • 11
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • DESMET, J., MAEYER, M. D., HAZES, B., AND LASTER, I. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356, 539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    Maeyer, M.D.2    Hazes, B.3    Laster, I.4
  • 12
    • 0036643430 scopus 로고    scopus 로고
    • Fast and accurate side-chain topology and energy refinement (faster) as a new method for protein structure optimization
    • DESMET, J., SPRIET, J., AND LASTER, I. 2002. Fast and accurate side-chain topology and energy refinement (faster) as a new method for protein structure optimization. Protein: Struct. Funct. Gen. 48, 31-43.
    • (2002) Protein: Struct. Funct. Gen. , vol.48 , pp. 31-43
    • Desmet, J.1    Spriet, J.2    Laster, I.3
  • 14
    • 0032613301 scopus 로고    scopus 로고
    • Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL
    • DUNBRACK JR., R. L. 1999. Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL. Protein: Struct. Funct. Gen. 3, 81-87.
    • (1999) Protein: Struct. Funct. Gen. , vol.3 , pp. 81-87
    • Dunbrack Jr., R.L.1
  • 15
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • DUNBRACK JR., R. L., AND COHEN, F. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6, 1661-1681.
    • (1997) Protein Sci. , vol.6 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.2
  • 17
    • 0028212927 scopus 로고
    • Efficient rotamer elimination applied to protein side-chains and related spin glasses
    • GOLDSTEIN, R. 1994. Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys. J. 66, 1335-1340.
    • (1994) Biophys. J. , vol.66 , pp. 1335-1340
    • Goldstein, R.1
  • 18
    • 0025978283 scopus 로고
    • Database algorithm for generating protein backbone and sidechain coordinates from a ca trace: Application to model building and detection of coordinate errors
    • HOLM, L., AND SANDER, C. 1991. Database algorithm for generating protein backbone and sidechain coordinates from a ca trace: Application to model building and detection of coordinate errors. J. Mol. Biol. 218, 183-194.
    • (1991) J. Mol. Biol. , vol.218 , pp. 183-194
    • Holm, L.1    Sander, C.2
  • 19
    • 0029497647 scopus 로고
    • On the approximation of shortest common supersequencesand longest common subsequences
    • JIANG, T., AND LI, M. 1995. On the approximation of shortest common supersequencesand longest common subsequences. SIAM J. Comput. 24, 5, 1122-1139.
    • (1995) SIAM J. Comput. , vol.24 , Issue.5 , pp. 1122-1139
    • Jiang, T.1    Li, M.2
  • 20
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • JONES, D. 1999. GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815.
    • (1999) J. Mol. Biol. , vol.287 , pp. 797-815
    • Jones, D.1
  • 21
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • KELLEY, L., MACCALLUM, R., AND STERNBERG, M. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 2, 499-520.
    • (2000) J. Mol. Biol. , vol.299 , Issue.2 , pp. 499-520
    • Kelley, L.1    Maccallum, R.2    Sternberg, M.3
  • 22
    • 16344382546 scopus 로고    scopus 로고
    • Solving and analyzing side-chain positioning problems using linear and integer programming
    • KINGSFORD, C. L., CHAZELLE, B., AND SINGH, M. 2005. Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics 21, 1028-1036.
    • (2005) Bioinformatics , vol.21 , pp. 1028-1036
    • Kingsford, C.L.1    Chazelle, B.2    Singh, M.3
  • 23
    • 0033665510 scopus 로고    scopus 로고
    • BALL-rapid software prototyping in computational molecular biology
    • KOHLBACHER, O., AND LENHOF, H. 2000. BALL-Rapid software prototyping in computational molecular biology. Bioinformatics 16, 9, 815-824.
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 815-824
    • Kohlbacher, O.1    Lenhof, H.2
  • 24
    • 0031717560 scopus 로고    scopus 로고
    • Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
    • LEACH, A., AND LEMON, A. 1998. Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm. Protein: Struct. Funct. Gen. 33, 227-239.
    • (1998) Protein: Struct. Funct. Gen. , vol.33 , pp. 227-239
    • Leach, A.1    Lemon, A.2
  • 25
    • 0026019108 scopus 로고
    • Prediction of protein side-chain conformation by packing optimization
    • LEE, C., AND SUBBIAH, S. 1991. Prediction of protein side-chain conformation by packing optimization. J. Mol. Biol. 217, 373-388.
    • (1991) J. Mol. Biol. , vol.217 , pp. 373-388
    • Lee, C.1    Subbiah, S.2
  • 26
    • 0034491129 scopus 로고    scopus 로고
    • Saturated blast: Detecting distant homology using automated multiple intermediate sequence blast search
    • LI, W., PIO, F., PAWLOWSKI, K., AND GODZIK, A. 2000. Saturated blast: Detecting distant homology using automated multiple intermediate sequence blast search. Bioinformatics 16, 1105-1110.
    • (2000) Bioinformatics , vol.16 , pp. 1105-1110
    • Li, W.1    Pio, F.2    Pawlowski, K.3    Godzik, A.4
  • 27
    • 0036149564 scopus 로고    scopus 로고
    • Side-chain modelling with an optimized scoring function
    • LIANG, S., AND GRISHIN, N. 2002. side-chain modelling with an optimized scoring function. Protein Sci. 11, 322-331.
    • (2002) Protein Sci. , vol.11 , pp. 322-331
    • Liang, S.1    Grishin, N.2
  • 28
    • 0030703027 scopus 로고    scopus 로고
    • Separators for sphere-packings and nearest neighbor graphs
    • MILLER, G. L., TENG, S., THURSTON, W., AND VAVASIS, S. A. 1997. Separators for sphere-packings and nearest neighbor graphs. J. ACM 44, 1, 1-29.
    • (1997) J. ACM , vol.44 , Issue.1 , pp. 1-29
    • Miller, G.L.1    Teng, S.2    Thurston, W.3    Vavasis, S.A.4
  • 29
    • 0035702809 scopus 로고    scopus 로고
    • Critical assessment of methods on protein structure prediction (CASP)-round IV
    • Dec.
    • MOULT, J., FIDELIS, F., ZEMLA, A., AND HUBBARD, T. 2001. Critical assessment of methods on protein structure prediction (CASP)-round IV. Proteins: Struct. Funct. Gen. 45, S5 (Dec.), 2-7.
    • (2001) Proteins: Struct. Funct. Gen. , vol.45 , Issue.S5 , pp. 2-7
    • Moult, J.1    Fidelis, F.2    Zemla, A.3    Hubbard, T.4
  • 30
    • 0242267517 scopus 로고    scopus 로고
    • Critical assessment of methods on protein structure prediction (CASP)-round v
    • Oct.
    • MOULT, J., FIDELIS, F., ZEMLA, A., AND HUBBARD, T. 2003. Critical assessment of methods on protein structure prediction (CASP)-round V. Proteins: Struct., Funct. Gen. 53, S6 (Oct.), 334-339.
    • (2003) Proteins: Struct., Funct. Gen. , vol.53 , Issue.S6 , pp. 334-339
    • Moult, J.1    Fidelis, F.2    Zemla, A.3    Hubbard, T.4
  • 31
    • 0032606039 scopus 로고    scopus 로고
    • Critical assessment of methods on protein structure prediction (CASP)-round III
    • Dec.
    • MOULT, J., HUBBARD, T., FIDELIS, F., AND PEDERSEN, J. 1999. Critical assessment of methods on protein structure prediction (CASP)-round III. Proteins: Struct. Funct. Gen. 37, S3 (Dec.), 2-6.
    • (1999) Proteins: Struct. Funct. Gen. , vol.37 , Issue.S3 , pp. 2-6
    • Moult, J.1    Hubbard, T.2    Fidelis, F.3    Pedersen, J.4
  • 33
    • 0037412183 scopus 로고    scopus 로고
    • Protein design is NP-hard
    • PIERCE, N., AND WINFREE, E. 2002. Protein design is NP-hard. Protein Engi. 15, 10, 779-782.
    • (2002) Protein Engi. , vol.15 , Issue.10 , pp. 779-782
    • Pierce, N.1    Winfree, E.2
  • 34
    • 0000673493 scopus 로고
    • Graph minors. II. Algorithmic aspects of tree-width
    • ROBERTSON, N., AND SEYMOUR, P. 1986. Graph minors. II. Algorithmic aspects of tree-width. J. Algorithms 7, 309-322.
    • (1986) J. Algorithms , vol.7 , pp. 309-322
    • Robertson, N.1    Seymour, P.2
  • 35
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • SALI, A., AND BLUNDELL, T. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 779-815.
    • (1993) J. Mol. Biol. , pp. 779-815
    • Sali, A.1    Blundell, T.2
  • 36
    • 0031794714 scopus 로고    scopus 로고
    • Determinants of side chain conformational preferences in protein structures
    • SAMUDRALA, R., AND MOULT, J. 1998. Determinants of side chain conformational preferences in protein structures. Protein Engi. 11, 991-997.
    • (1998) Protein Engi. , vol.11 , pp. 991-997
    • Samudrala, R.1    Moult, J.2
  • 37
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • SHI, J., TOM, L. B., AND KENJI, M. 2001. FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243-257.
    • (2001) J. Mol. Biol. , vol.310 , pp. 243-257
    • Shi, J.1    Tom, L.B.2    Kenji, M.3
  • 38
    • 0024816521 scopus 로고
    • Construction of side-chains in homology modelling: Application to the c-terminal lobe of rhizopuspepsin
    • SUMMERS, N., AND KARPLUS, M. 1989. Construction of side-chains in homology modelling: Application to the c-terminal lobe of rhizopuspepsin. J. Mol. Biol. 210, 785-811.
    • (1989) J. Mol. Biol. , vol.210 , pp. 785-811
    • Summers, N.1    Karplus, M.2
  • 39
    • 4143083332 scopus 로고    scopus 로고
    • Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
    • VON OHSEN, N., SOMMER, I., ZIMMER, R., AND LENGAUER, T. 2004. Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics 20, 14 (Sept.), 2228-35.
    • (2004) Bioinformatics , vol.20 , Issue.14 SEPT. , pp. 2228-2235
    • Von Ohsen, N.1    Sommer, I.2    Zimmer, R.3    Lengauer, T.4
  • 40
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limits of prediction for side-chain conformations
    • XIANG, Z., AND HONIG, B. 2001. Extending the accuracy limits of prediction for side-chain conformations. J. Mol. Biol. 311, 421-430.
    • (2001) J. Mol. Biol. , vol.311 , pp. 421-430
    • Xiang, Z.1    Honig, B.2
  • 43
    • 0031750906 scopus 로고    scopus 로고
    • An efficient computational method for globally optimal threadings
    • XU, Y., XU, D., AND UBERBACHER, E. 1998. An efficient computational method for globally optimal threadings. J. Comput. Biol. 5, 3, 597-614.
    • (1998) J. Comput. Biol. , vol.5 , Issue.3 , pp. 597-614
    • Xu, Y.1    Xu, D.2    Uberbacher, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.