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Volumn 12, Issue 9, 2003, Pages 2001-2014

A graph-theory algorithm for rapid protein side-chain prediction

Author keywords

Homology modeling; Rotamer library; SCWRL; Side chain prediction; Structure prediction

Indexed keywords

AB INITIO CALCULATION; ACCURACY; ALGORITHM; ARTICLE; COMPUTER PROGRAM; ENERGY; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; THEORY;

EID: 0042511005     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03154503     Document Type: Article
Times cited : (895)

References (47)
  • 2
    • 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., 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.J.1    Cohen, F.E.2    Dunbrack R.L., Jr.3
  • 3
    • 0029920337 scopus 로고    scopus 로고
    • Protein design automation
    • Dahiyat, B.I. and Mayo, S.L. 1996. Protein design automation. Protein Sci. 5: 895-903.
    • (1996) Protein Sci. , vol.5 , pp. 895-903
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 4
    • 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
    • De Maeyer, M., Desmet, J., and Lasters, I. 1997. All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of side-chains by dead-end elimination. Fold Des. 2: 53-66.
    • (1997) Fold Des. , vol.2 , pp. 53-66
    • De Maeyer, M.1    Desmet, J.2    Lasters, I.3
  • 5
    • 0034575680 scopus 로고    scopus 로고
    • The dead-end elimination theorem: Mathematical aspects, implementation, optimizations, evaluation, and performance
    • -. 2000. The dead-end elimination theorem: Mathematical aspects, implementation, optimizations, evaluation, and performance. Methods Mol. Biol. 143: 265-304.
    • (2000) Methods Mol. Biol. , vol.143 , pp. 265-304
  • 6
    • 0028858499 scopus 로고
    • De novo design of the hydrophobic cores of proteins
    • Desjarlais, J.R. and Handel, T.M. 1995. De novo design of the hydrophobic cores of proteins. Protein Sci. 4: 2006-2018.
    • (1995) Protein Sci. , vol.4 , pp. 2006-2018
    • Desjarlais, J.R.1    Handel, T.M.2
  • 7
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet, J., De Maeyer, M., Hazes, B., and Lasters, 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    De Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 8
    • 0031306143 scopus 로고    scopus 로고
    • Theoretical and algorithmical optimization of the dead-end elimination theorem
    • Desmet, J., De Maeyer, M., and Lasters, I. 1997. Theoretical and algorithmical optimization of the dead-end elimination theorem. Pac. Symp. Biocomput. 1997: 122-133.
    • (1997) Pac. Symp. Biocomput. , vol.1997 , pp. 122-133
    • Desmet, J.1    De Maeyer, M.2    Lasters, I.3
  • 9
    • 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 Lasters, I. 2002. Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization. Proteins 48: 31-43.
    • (2002) Proteins , vol.48 , pp. 31-43
    • Desmet, J.1    Spriet, J.2    Lasters, I.3
  • 10
    • 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. Proteins 3: 81-87.
    • (1999) Proteins , vol.3 , pp. 81-87
    • Dunbrack R.L., Jr.1
  • 11
    • 0036667731 scopus 로고    scopus 로고
    • Rotamer libraries in the 21st century
    • -. 2002. Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 12: 431-440.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 431-440
  • 12
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack Jr., R.L. and Cohen, F.E. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6: 1661-1681.
    • (1997) Protein Sci. , vol.6 , pp. 1661-1681
    • Dunbrack R.L., Jr.1    Cohen, F.E.2
  • 13
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins: Application to side-chain prediction
    • Dunbrack Jr., R.L. and Karplus, M. 1993. Backbone-dependent rotamer library for proteins: Application to side-chain prediction. J. Mol. Biol. 230: 543-574.
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-574
    • Dunbrack R.L., Jr.1    Karplus, M.2
  • 14
    • 0028429178 scopus 로고
    • Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
    • -. 1994, Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nature Struct. Biol. 1: 334-340.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 334-340
  • 15
    • 0028212927 scopus 로고
    • Efficient rotamer elimination applied to protein side-chains and related spin glasses
    • Goldstein, R.F. 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.F.1
  • 16
    • 0033200183 scopus 로고    scopus 로고
    • Branch-and-terminate: A combinatorial optimization algorithm for protein design
    • Gordon, D.B. and Mayo, S.L. 1999. Branch-and-terminate: A combinatorial optimization algorithm for protein design. Structure Fold Des. 7: 1089-1098.
    • (1999) Structure Fold Des. , vol.7 , pp. 1089-1098
    • Gordon, D.B.1    Mayo, S.L.2
  • 17
    • 0025978283 scopus 로고
    • Database algorithm for generating protein back-bone 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 back-bone 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
  • 18
    • 0029058162 scopus 로고
    • Side-chain prediction by neural networks and simulated annealing optimization
    • Hwang, J.K. and Liao, W.F. 1995. Side-chain prediction by neural networks and simulated annealing optimization. Protein Eng. 8: 363-370.
    • (1995) Protein Eng. , vol.8 , pp. 363-370
    • Hwang, J.K.1    Liao, W.F.2
  • 19
    • 0029591934 scopus 로고
    • Finding the global minimum: A fuzzy end elimination implementation
    • Keller, D.A., Shibata, M., Marcus, E., Ornstein, R.L., and Rein, R. 1995. Finding the global minimum: A fuzzy end elimination implementation. Protein Eng. 8: 893-904.
    • (1995) Protein Eng. , vol.8 , pp. 893-904
    • Keller, D.A.1    Shibata, M.2    Marcus, E.3    Ornstein, R.L.4    Rein, R.5
  • 20
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • Kelley, L.A., MacCallum, R.M., and Stemberg, M.J. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299: 499-520.
    • (2000) J. Mol. Biol. , vol.299 , pp. 499-520
    • Kelley, L.A.1    MacCallum, R.M.2    Stemberg, M.J.3
  • 21
    • 0029565303 scopus 로고
    • A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling
    • Koehl, P. and Delarue, M. 1995. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling. Nat. Struct. Biol. 2: 163-170.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 163-170
    • Koehl, P.1    Delarue, M.2
  • 22
    • 0028304155 scopus 로고
    • Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry
    • Kono, H. and Doi, J. 1994. Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry. Proteins 19: 244-255.
    • (1994) Proteins , vol.19 , pp. 244-255
    • Kono, H.1    Doi, J.2
  • 24
    • 0027493639 scopus 로고
    • The fuzzy-end elimination theorem: Correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem
    • Lasters, I. and Desmet, J. 1993. The fuzzy-end elimination theorem: Correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem. Protein Eng. 6: 717-722.
    • (1993) Protein Eng. , vol.6 , pp. 717-722
    • Lasters, I.1    Desmet, J.2
  • 25
    • 0028826985 scopus 로고
    • Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side-chains
    • Lasters, I., DeMaeyer, M., and Desmet, J. 1995. Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side-chains. Protein Eng. 8: 815-822.
    • (1995) Protein Eng. , vol.8 , pp. 815-822
    • Lasters, I.1    DeMaeyer, M.2    Desmet, J.3
  • 26
    • 0028140474 scopus 로고
    • Prediction of protein side-chain conformations from local three-dimensional homology relationships
    • Laughton, C.A. 1994. Prediction of protein side-chain conformations from local three-dimensional homology relationships. J. Mol. Biol. 235: 1088-1097.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1088-1097
    • Laughton, C.A.1
  • 27
    • 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
  • 28
    • 0036149564 scopus 로고    scopus 로고
    • Side-chain modeling with an optimized scoring function
    • Liang, S. and Grishin, N.V. 2002. Side-chain modeling with an optimized scoring function. Protein Sci. 11: 322-331.
    • (2002) Protein Sci. , vol.11 , pp. 322-331
    • Liang, S.1    Grishin, N.V.2
  • 29
    • 0035896029 scopus 로고    scopus 로고
    • Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics
    • Looger, L.L. and Hellinga, H.W. 2001. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics. J. Mol. Biol. 307: 429-445.
    • (2001) J. Mol. Biol. , vol.307 , pp. 429-445
    • Looger, L.L.1    Hellinga, H.W.2
  • 31
    • 0023521842 scopus 로고
    • Analysis of the relationship between side-chain conformation and secondary structure in globular proteins
    • McGregor, M.J., Islam, S.A., and Sternberg, M.J.E. 1987. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198: 295-310.
    • (1987) J. Mol. Biol. , vol.198 , pp. 295-310
    • McGregor, M.J.1    Islam, S.A.2    Sternberg, M.J.E.3
  • 32
    • 0032732306 scopus 로고    scopus 로고
    • Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model
    • Mendes, J., Baptista, A.M., Carrondo, M.A., and Soares, C.M. 1999a. Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model. Proteins 37: 530-543.
    • (1999) Proteins , vol.37 , pp. 530-543
    • Mendes, J.1    Baptista, A.M.2    Carrondo, M.A.3    Soares, C.M.4
  • 33
    • 0033042104 scopus 로고    scopus 로고
    • Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction
    • Mendes, J., Soares, C.M., and Carrondo, M.A. 1999b. Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. Biopolymers 50: 111-131.
    • (1999) Biopolymers , vol.50 , pp. 111-131
    • Mendes, J.1    Soares, C.M.2    Carrondo, M.A.3
  • 34
    • 0034748018 scopus 로고    scopus 로고
    • Implicit solvation in the self-consistent mean field theory method: Side-chain modeling and prediction of folding free energies of protein mutants
    • Mendes, J., Baptista, A.M., Carrondo, M.A., and Soares, C.M. 2001a. Implicit solvation in the self-consistent mean field theory method: Side-chain modeling and prediction of folding free energies of protein mutants. J. Comp. Aided. Mol. Design 15: 721-740.
    • (2001) J. Comp. Aided. Mol. Design , vol.15 , pp. 721-740
    • Mendes, J.1    Baptista, A.M.2    Carrondo, M.A.3    Soares, C.M.4
  • 35
    • 0034957437 scopus 로고    scopus 로고
    • Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure
    • Mendes, J., Nagarajaram, H.A., Soares, C.M., Blundell, T.L., and Carrondo, M.A. 2001b. Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure. Biopolymers 59: 72-86.
    • (2001) Biopolymers , vol.59 , pp. 72-86
    • Mendes, J.1    Nagarajaram, H.A.2    Soares, C.M.3    Blundell, T.L.4    Carrondo, M.A.5
  • 36
    • 0001114311 scopus 로고    scopus 로고
    • Conformational splitting: A more powerful criterion for dead-end elimination
    • Pierce, N.A., Spriet, J.A., Desmet, J., and Mayo, S.L, 1999. Conformational splitting: A more powerful criterion for dead-end elimination. J. Comp. Chem. 21: 999-1009.
    • (1999) J. Comp. Chem. , vol.21 , pp. 999-1009
    • Pierce, N.A.1    Spriet, J.A.2    Desmet, J.3    Mayo, S.L.4
  • 37
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder, J.W. and Richards, F.M. 1987. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193: 775-792.
    • (1987) J. Mol. Biol. , vol.193 , pp. 775-792
    • Ponder, J.W.1    Richards, F.M.2
  • 38
    • 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 Eng. 11: 991-997.
    • (1998) Protein Eng. , vol.11 , pp. 991-997
    • Samudrala, R.1    Moult, J.2
  • 39
    • 0024816521 scopus 로고
    • Construction of side-chains in homology modelling: Application to the C-terminal lobe of rhizopuspepsin
    • Summers, N.L. 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.L.1    Karplus, M.2
  • 40
    • 0001790593 scopus 로고
    • Depth first search and linear graph algorithms
    • Tarjan, R. 1972. Depth first search and linear graph algorithms. SIAM J. Comput. 1: 146-160.
    • (1972) SIAM J. Comput. , vol.1 , pp. 146-160
    • Tarjan, R.1
  • 41
    • 0026179489 scopus 로고
    • A new approach to the rapid determination of protein side chain conformations
    • Tuffery, P., Etchebest, C. Hazout, S., and Lavery, R. 1991. A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn. 8: 1267-1289.
    • (1991) J. Biomol. Struct. Dyn. , vol.8 , pp. 1267-1289
    • Tuffery, P.1    Etchebest, C.2    Hazout, S.3    Lavery, R.4
  • 42
    • 0034625322 scopus 로고    scopus 로고
    • Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design
    • Voigt, C.A., Gordon, D.B., and Mayo, S.L. 2000. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. J. Mol. Biol. 299: 789-803.
    • (2000) J. Mol. Biol. , vol.299 , pp. 789-803
    • Voigt, C.A.1    Gordon, D.B.2    Mayo, S.L.3
  • 43
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • in press
    • Wang, G. and Dunbrack Jr., R.L. 2003. PISCES: A protein sequence culling server. Bioinformatics (in press).
    • (2003) Bioinformatics
    • Wang, G.1    Dunbrack R.L., Jr.2
  • 44
    • 0027480460 scopus 로고
    • Modeling side-chain conformation for homologous proteins using an energy-based rotamer search
    • Wilson, C., Gregoret, L., and Agard, D. 1993. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J. Mol. Biol. 229: 996-1006.
    • (1993) J. Mol. Biol. , vol.229 , pp. 996-1006
    • Wilson, C.1    Gregoret, L.2    Agard, D.3
  • 46
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word, J.M., Lovell, S.C., Richardson, J.S., and Richardson, D.C. 1999b. Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285: 1735-1747.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 47
    • 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


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