메뉴 건너뛰기




Volumn 16, Issue 4, 2004, Pages 380-392

A semidefinite programming approach to side chain positioning with new rounding strategies

Author keywords

Computational biology; Semidefinite programming; Side chain positioning

Indexed keywords

ALGORITHMS; AMINO ACIDS; COMPUTATIONAL METHODS; HEURISTIC METHODS; MATHEMATICAL MODELS; MOLECULAR BIOLOGY; PROBLEM SOLVING;

EID: 10044241588     PISSN: 10919856     EISSN: 15265528     Source Type: Journal    
DOI: 10.1287/ijoc.1040.0096     Document Type: Article
Times cited : (75)

References (47)
  • 1
    • 0003169116 scopus 로고
    • Interior point methods in semidefinite programming with applications to combinatorial optimization
    • Alizadeh, F. 1995. Interior point methods in semidefinite programming with applications to combinatorial optimization. SIAM J. Optim. 5 13-51.
    • (1995) SIAM J. Optim. , vol.5 , pp. 13-51
    • Alizadeh, F.1
  • 2
    • 0001262835 scopus 로고    scopus 로고
    • Approximating the independence number via the Θ-function
    • Alon, N., N. Kahale. 1998. Approximating the independence number via the Θ-function. Math. Programming 80 253-264.
    • (1998) Math. Programming , vol.80 , pp. 253-264
    • Alon, N.1    Kahale, N.2
  • 4
    • 0031651077 scopus 로고    scopus 로고
    • Probabilistic checking of proofs: A new characterization of NP
    • Arora, S., M. Safra. 1998. Probabilistic checking of proofs: A new characterization of NP. J. ACM 45 70-122.
    • (1998) J. ACM , vol.45 , pp. 70-122
    • Arora, S.1    Safra, M.2
  • 5
    • 0032058198 scopus 로고    scopus 로고
    • Proof verification and hardness of approximation problems
    • Arora, S., C. Lund, R. Motwani, M. Sudan, M. Szegedy. 1998. Proof verification and hardness of approximation problems. J. ACM 45 501-555.
    • (1998) J. ACM , vol.45 , pp. 501-555
    • Arora, S.1    Lund, C.2    Motwani, R.3    Sudan, M.4    Szegedy, M.5
  • 7
    • 0033294696 scopus 로고    scopus 로고
    • Mixed linear and semidefinite programming for combinatorial and quadratic optimization
    • Benson, S. J., Y. Ye, X. Zhang. 1999. Mixed linear and semidefinite programming for combinatorial and quadratic optimization. Optim. Methods Software 11 515-544.
    • (1999) Optim. Methods Software , vol.11 , pp. 515-544
    • Benson, S.J.1    Ye, Y.2    Zhang, X.3
  • 8
    • 0005325563 scopus 로고    scopus 로고
    • Semidefinite relaxations, multivariate normal distributions, and order statistics
    • D.-Z. Du, P. M. Pardalos, eds. Kluwer Academic Publishers, New York
    • Bertsimas, D., Y. Ye. 1998. Semidefinite relaxations, multivariate normal distributions, and order statistics. D.-Z. Du, P. M. Pardalos, eds. Handbook of Combinatorial Optimization, Vol. 3. Kluwer Academic Publishers, New York, 1-19.
    • (1998) Handbook of Combinatorial Optimization , vol.3 , pp. 1-19
    • Bertsimas, D.1    Ye, Y.2
  • 9
    • 0023601196 scopus 로고
    • Eigenvalues and graph bisection: An average-case analysis
    • IEEE Computer Society Press, Washington, D.C.
    • Boppana, R. B. 1987. Eigenvalues and graph bisection: An average-case analysis. Proc. Twenty-eighth Annual Sympos. Foundation Comput, Sci., IEEE Computer Society Press, Washington, D.C., 280-285.
    • (1987) Proc. Twenty-eighth Annual Sympos. Foundation Comput, Sci. , pp. 280-285
    • Boppana, R.B.1
  • 10
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A homology modeling tool
    • Bower, M. J., F. E. Cohen, R. L. Dunbrack, Jr. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A homology modeling tool. J. Molecular Biol. 267 1268-1282.
    • (1997) J. Molecular Biol. , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack Jr., R.L.3
  • 12
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat, B. I., S. L. Mayo. 1997. De novo protein design: Fully automated sequence selection. Science 278 82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 13
    • 0002114152 scopus 로고
    • The "dead end elimination" theorem as a new approach to the side-chain packing problem
    • K. Merz, S. LeGrand, eds. Birkhäuser, Boston, MA
    • Desmet, J., M. De Maeyer, I. Lasters. 1994. The "dead end elimination" theorem as a new approach to the side-chain packing problem. K. Merz, S. LeGrand, eds. The Protein Folding Problem and Tertiary Structure Prediction. Birkhäuser, Boston, MA, 307-337.
    • (1994) The Protein Folding Problem and Tertiary Structure Prediction , pp. 307-337
    • Desmet, J.1    De Maeyer, M.2    Lasters, I.3
  • 14
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet, J., M. De Maeyer, B. Hazes, I. Lasters. 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
  • 15
    • 0011504283 scopus 로고
    • Algorithms for partitioning of graphs and computer logic based on eigenvectors of connection matrices
    • Donath, W. E., A. Hoffman. 1972. Algorithms for partitioning of graphs and computer logic based on eigenvectors of connection matrices. IBM Tech. Disclosure Bull. 15 938-944.
    • (1972) IBM Tech. Disclosure Bull. , vol.15 , pp. 938-944
    • Donath, W.E.1    Hoffman, A.2
  • 16
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins: Application to side-chain prediction
    • Dunbrack, Jr., R. L., M. Karplus. 1993. Backbone-dependent rotamer library for proteins: Application to side-chain prediction. J. Molecular Biol. 230 543-574.
    • (1993) J. Molecular Biol. , vol.230 , pp. 543-574
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 17
    • 68549106477 scopus 로고    scopus 로고
    • Side chain-positioning as an integer programming problem
    • BRICS, University of Aarhus, Denmark
    • Eriksson, O., Y. Zhou, A. Elofsson. 2001. Side chain-positioning as an integer programming problem. Proc. First Workshop Algorithms BioInformatics., BRICS, University of Aarhus, Denmark, 129-141.
    • (2001) Proc. First Workshop Algorithms BioInformatics , pp. 129-141
    • Eriksson, O.1    Zhou, Y.2    Elofsson, A.3
  • 18
    • 0032313643 scopus 로고    scopus 로고
    • Heuristics for finding large independent sets, with applications to coloring semi-random graphs
    • IEEE Computer Society, Los Alamitos, CA
    • Feige, U., J. Kilian. 1998. Heuristics for finding large independent sets, with applications to coloring semi-random graphs. Proc. Thirty-ninth Annual Sympos. Foundation Comput. Sci., IEEE Computer Society, Los Alamitos, CA, 674-683.
    • (1998) Proc. Thirty-ninth Annual Sympos. Foundation Comput. Sci. , pp. 674-683
    • Feige, U.1    Kilian, J.2
  • 20
    • 0346613559 scopus 로고    scopus 로고
    • Improved approximation algorithms for MAX k-CUT and MAX BISECTION
    • Frieze, A., M. Jerrum. 1997. Improved approximation algorithms for MAX k-CUT and MAX BISECTION. Algorithmica 18 61-77.
    • (1997) Algorithmica , vol.18 , pp. 61-77
    • Frieze, A.1    Jerrum, M.2
  • 21
    • 0041140580 scopus 로고    scopus 로고
    • Numerical evaluation of SDPA
    • Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, Oh-Okayama, Meguro-ku, Tokyo, Japan
    • Fujisawa, K., M. Fukuda, M. Kojima, K. Nakata. 1997. Numerical evaluation of SDPA. Technical report B-330, Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, Oh-Okayama, Meguro-ku, Tokyo 152, Japan.
    • (1997) Technical Report , vol.B-330 , pp. 152
    • Fujisawa, K.1    Fukuda, M.2    Kojima, M.3    Nakata, K.4
  • 22
    • 84893574327 scopus 로고
    • Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming
    • Goemans, M. X., D. P. Williamson. 1995. Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming. J. ACM 42 1115-1145.
    • (1995) J. ACM , vol.42 , pp. 1115-1145
    • Goemans, M.X.1    Williamson, D.P.2
  • 23
    • 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
  • 24
    • 0001686478 scopus 로고    scopus 로고
    • Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem
    • Gordon, D. B., S. L. Mayo. 1998. Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem. J. Comput. Chem. 19 1505-1514.
    • (1998) J. Comput. Chem. , vol.19 , pp. 1505-1514
    • Gordon, D.B.1    Mayo, S.L.2
  • 26
    • 10044265971 scopus 로고    scopus 로고
    • ILOG CPLEX. 2000. ILOG CPLEX 7.1. http://www.ilog.com/.
    • (2000) ILOG CPLEX 7.1
  • 27
    • 0032028848 scopus 로고    scopus 로고
    • Approximate graph coloring by semidefinite programming
    • Karger, D., R. Motwani, M. Sudan. 1998. Approximate graph coloring by semidefinite programming. J. ACM 45 246-265.
    • (1998) J. ACM , vol.45 , pp. 246-265
    • Karger, D.1    Motwani, R.2    Sudan, M.3
  • 28
    • 0033665510 scopus 로고    scopus 로고
    • BALL - Rapid software prototyping in computational molecular biology
    • Kohlbacher, O., H.-P. Lenhof. 2000. BALL - rapid software prototyping in computational molecular biology. Bioinformatics 16 815-824.
    • (2000) Bioinformatics , vol.16 , pp. 815-824
    • Kohlbacher, O.1    Lenhof, H.-P.2
  • 29
    • 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., M. De Maeyer, J. Desmet. 1995. Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains. Protein Engrg. 8 815-822.
    • (1995) Protein Engrg. , vol.8 , pp. 815-822
    • Lasters, I.1    De Maeyer, M.2    Desmet, J.3
  • 30
    • 0036542560 scopus 로고    scopus 로고
    • A new approach for weighted constraint satisfaction
    • Lau, H. C. 2002. A new approach for weighted constraint satisfaction. Constraints 7 151-165.
    • (2002) Constraints , vol.7 , pp. 151-165
    • Lau, H.C.1
  • 31
    • 84947906598 scopus 로고    scopus 로고
    • Randomized approximation of the constraint satisfaction problem
    • R. Karlsson, A. Lingas, eds. Springer, Berlin, Germany
    • Lau, H. C., O. Watanabe. 1996. Randomized approximation of the constraint satisfaction problem. R. Karlsson, A. Lingas, eds. Proc. Fifth Scandinavian Workshop Algorithm Theory, Springer, Berlin, Germany, 76-87.
    • (1996) Proc. Fifth Scandinavian Workshop Algorithm Theory , pp. 76-87
    • Lau, H.C.1    Watanabe, O.2
  • 32
    • 0031717560 scopus 로고    scopus 로고
    • Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
    • Leach, A. R., A. P. Lemon. 1998. Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm. Proteins 33 227-239.
    • (1998) Proteins , vol.33 , pp. 227-239
    • Leach, A.R.1    Lemon, A.P.2
  • 33
    • 0028223845 scopus 로고
    • Predicting protein mutant energetics by self-consistent ensemble optimization
    • Lee, C. 1994. Predicting protein mutant energetics by self-consistent ensemble optimization. J. Molecular Biol. 236 918-939.
    • (1994) J. Molecular Biol. , vol.236 , pp. 918-939
    • Lee, C.1
  • 34
    • 0026019108 scopus 로고
    • Prediction of protein side-chain conformation by packing optimization
    • Lee, C., S. Subbiah. 1991. Prediction of protein side-chain conformation by packing optimization. J. Molecular Biol. 217 373-388.
    • (1991) J. Molecular Biol. , vol.217 , pp. 373-388
    • Lee, C.1    Subbiah, S.2
  • 35
    • 0024529940 scopus 로고
    • Structural principles of α/β barrel proteins: The packing of the interior of the sheet
    • Lesk, A. M., C.-I. Brändén, C. Chothia. 1989. Structural principles of α/β barrel proteins: The packing of the interior of the sheet. Proteins 5 139-148.
    • (1989) Proteins , vol.5 , pp. 139-148
    • Lesk, A.M.1    Brändén, C.-I.2    Chothia, C.3
  • 36
    • 0018292109 scopus 로고
    • On the Shannon capacity of a graph
    • Lovász, L. 1979. On the Shannon capacity of a graph. IEEE Trans. Inform. Theory 25 1-7.
    • (1979) IEEE Trans. Inform. Theory , vol.25 , pp. 1-7
    • Lovász, L.1
  • 37
    • 0031779918 scopus 로고    scopus 로고
    • Design, structure and stability of a hyperthermophilic protein variant
    • Malakauskas, S. M., S. L. Mayo. 1998. Design, structure and stability of a hyperthermophilic protein variant. Nature Structural Biol. 5 470-475.
    • (1998) Nature Structural Biol. , vol.5 , pp. 470-475
    • Malakauskas, S.M.1    Mayo, S.L.2
  • 38
    • 0034615784 scopus 로고    scopus 로고
    • Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein
    • Mueller, U., D. Perl, F. X. Schmid, U. Heinemann. 2000. Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein. J. Molecular Biol. 297 975-988.
    • (2000) J. Molecular Biol. , vol.297 , pp. 975-988
    • Mueller, U.1    Perl, D.2    Schmid, F.X.3    Heinemann, U.4
  • 40
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls, A., K. A. Sharp, B. Honig. 1991. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11 281-296.
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 41
    • 0037412183 scopus 로고    scopus 로고
    • Protein design is NP-hard
    • Pierce, N. A., E. Winfree. 2002. Protein design is NP-hard. Protein Engrg. 15 779-782.
    • (2002) Protein Engrg. , vol.15 , pp. 779-782
    • Pierce, N.A.1    Winfree, E.2
  • 42
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder, J. W., F. M. Richards. 1987. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Molecular Biol. 193 775-791.
    • (1987) J. Molecular Biol. , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 43
    • 51249173817 scopus 로고
    • Randomized rounding: A technique for provably good algorithms and algorithmic proofs
    • Raghavan, P., C. Thompson. 1987. Randomized rounding: A technique for provably good algorithms and algorithmic proofs. Combinatorica 7 365-374.
    • (1987) Combinatorica , vol.7 , pp. 365-374
    • Raghavan, P.1    Thompson, C.2
  • 44
    • 0141977598 scopus 로고    scopus 로고
    • A case study of de-randomization methods for combinatorial approximation problems
    • Rolim, J. D. P., L. Trevisan. 1998. A case study of de-randomization methods for combinatorial approximation problems. J. Combin. Optim. 2 219-236.
    • (1998) J. Combin. Optim. , vol.2 , pp. 219-236
    • Rolim, J.D.P.1    Trevisan, L.2
  • 46
    • 0030106462 scopus 로고    scopus 로고
    • Semidefinite programming
    • Vandenberghe, L., S. Boyd. 1996. Semidefinite programming. SIAM Rev. 38 49-95.
    • (1996) SIAM Rev. , vol.38 , pp. 49-95
    • Vandenberghe, L.1    Boyd, S.2
  • 47
    • 0032631766 scopus 로고    scopus 로고
    • Outward rotations: A tool for rounding solutions of semidefinite programming relaxations, with applications to MAX CUT and other problems
    • ACM Press, New York
    • Zwick, U. 1999. Outward rotations: A tool for rounding solutions of semidefinite programming relaxations, with applications to MAX CUT and other problems. Proc. Thirty-first Annual ACM Sympos. Theory Comput., ACM Press, New York, 679-687.
    • (1999) Proc. Thirty-first Annual ACM Sympos. Theory Comput. , pp. 679-687
    • Zwick, U.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.