메뉴 건너뛰기




Volumn 5202 LNCS, Issue , 2008, Pages 82-96

Protein structure prediction with large neighborhood constraint programming search

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO; CHALLENGING PROBLEMS; COMPLEX LATTICES; CONSTRAINT PROGRAMMINGS; FACE CENTERED CUBIC LATTICES; FCC LATTICES; HYBRID ALGORITHMS; LARGE NEIGHBORHOOD SEARCHES; LARGE NEIGHBORHOODS; LATTICE MODELS; NATIVE STATES; PROTEIN STRUCTURE PREDICTIONS; SEARCH ALGORITHMS;

EID: 56449120900     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-85958-1_6     Document Type: Conference Paper
Times cited : (13)

References (52)
  • 1
    • 84986522918 scopus 로고    scopus 로고
    • Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A.: ICM: a new method for structure modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comp. Chem. 15. 488-506 (1994)
    • Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A.: ICM: a new method for structure modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comp. Chem. 15. 488-506 (1994)
  • 2
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen, C.B.: Principles that govern the folding of protein chains. Science 181 (1973)
    • (1973) Science , vol.181
    • Anfinsen, C.B.1
  • 3
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • Arnold, K., Bordoli, L., Kopp, J., Schwede, T.: The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22(2) (2006)
    • (2006) Bioinformatics , vol.22 , Issue.2
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 4
    • 0035366744 scopus 로고    scopus 로고
    • The protein structure prediction problem: A constraint optimization approach using a new lower bound
    • Backofen, R.: The protein structure prediction problem: A constraint optimization approach using a new lower bound. Constraints 6(2-3), 223-255 (2001)
    • (2001) Constraints , vol.6 , Issue.2-3 , pp. 223-255
    • Backofen, R.1
  • 5
    • 0032891933 scopus 로고    scopus 로고
    • Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets
    • Backofen, R., Will, S., Bornberg-Bauer, E.: Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. Bioinformatics 15(3), 234-242(1999)
    • (1999) Bioinformatics , vol.15 , Issue.3 , pp. 234-242
    • Backofen, R.1    Will, S.2    Bornberg-Bauer, E.3
  • 6
    • 0033642235 scopus 로고    scopus 로고
    • Algorithmic approach to quantifying the hydrophobic force contribution in protein folding
    • Backofen, R., Will, S., Clote, P.: Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. In: Pacific Symposium on Biocomputing, vol. 5, pp. 92-103 (2000)
    • (2000) Pacific Symposium on Biocomputing , vol.5 , pp. 92-103
    • Backofen, R.1    Will, S.2    Clote, P.3
  • 8
    • 0348155923 scopus 로고    scopus 로고
    • Backofen, R., Will, S.: A constraint-based approach to structure prediction for simplified protein models that outperforms other existing methods. In: Palamidessi, C. (ed.) ICLP 2003. LNCS, 2916, pp. 49-71. Springer, Heidelberg (2003)
    • Backofen, R., Will, S.: A constraint-based approach to structure prediction for simplified protein models that outperforms other existing methods. In: Palamidessi, C. (ed.) ICLP 2003. LNCS, vol. 2916, pp. 49-71. Springer, Heidelberg (2003)
  • 9
    • 0031897962 scopus 로고    scopus 로고
    • Protein folding in the hydrophobic-hydrophilic (hp) model is NP-complete
    • Berger, B., Leighton, T.: Protein folding in the hydrophobic-hydrophilic (hp) model is NP-complete. Journal of Computational Biology 5, 27-40 (1998)
    • (1998) Journal of Computational Biology , vol.5 , pp. 27-40
    • Berger, B.1    Leighton, T.2
  • 10
    • 0036616218 scopus 로고    scopus 로고
    • Berman, H.M., Battistuz, T., Bhat, T.N., Bluhm, W.F., Bourne, P.E., Burkhardt, K., Feng, Z., Gilliland, G.L., Iype, L., Jain, S., Pagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J.D., Zardecki, C.: The Protein Data Bank. Acta Crystallogr. D. Biol. Crystallogr. 58(Pt), 899-907 (2002)
    • Berman, H.M., Battistuz, T., Bhat, T.N., Bluhm, W.F., Bourne, P.E., Burkhardt, K., Feng, Z., Gilliland, G.L., Iype, L., Jain, S., Pagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J.D., Zardecki, C.: The Protein Data Bank. Acta Crystallogr. D. Biol. Crystallogr. 58(Pt), 899-907 (2002)
  • 11
    • 0030709797 scopus 로고    scopus 로고
    • Bornberg-Bauer, E.: Chain growth algorithms for HP-type lattice proteins. In: RECOMB, pp. 47-55. ACM Press, New York (1997)
    • Bornberg-Bauer, E.: Chain growth algorithms for HP-type lattice proteins. In: RECOMB, pp. 47-55. ACM Press, New York (1997)
  • 12
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley, P., Misura, K.M., Baker, D.: Toward high-resolution de novo structure prediction for small proteins. Science 309(5742), 1868-1871 (2005)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 13
    • 56449100565 scopus 로고    scopus 로고
    • Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search
    • to appear
    • Cebrian, M., Dotu, I., Van Hentenryck, P., Clote, P.: Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search. In: AAAI 2008 (to appear, 2008)
    • (2008) AAAI
    • Cebrian, M.1    Dotu, I.2    Van Hentenryck, P.3    Clote, P.4
  • 15
    • 0001459730 scopus 로고    scopus 로고
    • Packing challenge mastered at last
    • Cipra, B.: Packing challenge mastered at last. Science 281, 1267 (1998)
    • (1998) Science , vol.281 , pp. 1267
    • Cipra, B.1
  • 18
    • 13244275057 scopus 로고    scopus 로고
    • Constraint Logic Programming approach to protein structure prediction
    • Dal Palu, A., Dovier, A., Fogolari, F.: Constraint Logic Programming approach to protein structure prediction. BMC. Bioinformatics 5, 186 (2004)
    • (2004) BMC. Bioinformatics , vol.5 , pp. 186
    • Dal Palu, A.1    Dovier, A.2    Fogolari, F.3
  • 19
    • 34548136236 scopus 로고    scopus 로고
    • An evaluation of automated homology modelling methods at low target template sequence similarity
    • Dalton, J.A., Jackson, R.M.: An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics 23(15), 1901-1908 (2007)
    • (2007) Bioinformatics , vol.23 , Issue.15 , pp. 1901-1908
    • Dalton, J.A.1    Jackson, R.M.2
  • 20
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan, Y, et al.: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24(16), 1999-2012 (2003)
    • (2003) J. Comput. Chem , vol.24 , Issue.16 , pp. 1999-2012
    • Duan, Y.1
  • 21
    • 34249824268 scopus 로고    scopus 로고
    • Computational methods in protein structure prediction
    • Floudas, C.A.: Computational methods in protein structure prediction. Biotechnol. Bioeng. 97(2), 207-213 (2007)
    • (2007) Biotechnol. Bioeng , vol.97 , Issue.2 , pp. 207-213
    • Floudas, C.A.1
  • 22
    • 0000355428 scopus 로고
    • Respective roles of short- and long-range interactions in protein folding
    • Go, N., Taketomi, H.: Respective roles of short- and long-range interactions in protein folding. Proc. Natl. Acad. Sci. U.S.A. 75(2), 559-563 (1978)
    • (1978) Proc. Natl. Acad. Sci. U.S.A , vol.75 , Issue.2 , pp. 559-563
    • Go, N.1    Taketomi, H.2
  • 23
    • 0018475814 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation. III. Effect of short-range interactions
    • Go, N., Taketomi, H.: Studies on protein folding, unfolding and fluctuations by computer simulation. III. Effect of short-range interactions. Int. J. Pept. Protein. Res. 13(3) ( 1979)
    • (1979) Int. J. Pept. Protein. Res , vol.13 , Issue.3
    • Go, N.1    Taketomi, H.2
  • 24
    • 39149143625 scopus 로고    scopus 로고
    • A comparative study of the reported performance of ab initio protein structure prediction algorithms
    • Helles, G.: A comparative study of the reported performance of ab initio protein structure prediction algorithms. J. R. Soc. Interface 5(21), 387-396 (2008)
    • (2008) J. R. Soc. Interface , vol.5 , Issue.21 , pp. 387-396
    • Helles, G.1
  • 25
    • 0025978283 scopus 로고
    • Database algorithm for generating protein backbone and side-chain coordinates from a C alpha trace application to model building and detection of co-ordinate errors
    • Holm, L., Sander, C.: Database algorithm for generating protein backbone and side-chain coordinates from a C alpha trace application to model building and detection of co-ordinate errors. J. Mol. Biol. 218(1), 183-194 (1991)
    • (1991) J. Mol. Biol , vol.218 , Issue.1 , pp. 183-194
    • Holm, L.1    Sander, C.2
  • 26
    • 0141978673 scopus 로고    scopus 로고
    • Comparative protein structure modeling by iterative alignment, model building and model assessment
    • 200.3
    • John, B., Sali, A.: Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic. Acids. Res. 31(14), 3982-3992 (200.3)
    • Nucleic. Acids. Res , vol.31 , Issue.14 , pp. 3982-3992
    • John, B.1    Sali, A.2
  • 27
    • 0037472756 scopus 로고    scopus 로고
    • Prediction of β-sheet topology and disulfide bridges in polypeptides
    • Klepeis, J.L., Floudas, C.A.: Prediction of β-sheet topology and disulfide bridges in polypeptides. Journal of Computational Chemistry 24(2), 191-208 (2002)
    • (2002) Journal of Computational Chemistry , vol.24 , Issue.2 , pp. 191-208
    • Klepeis, J.L.1    Floudas, C.A.2
  • 28
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J., Doolittle, R.F.: A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157(1), 105-132 (1982)
    • (1982) J. Mol. Biol , vol.157 , Issue.1 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 30
    • 0028015988 scopus 로고
    • The protein threading problem with sequence amino acid interaction preferences is NP-complete
    • Lathrop, R.H.: The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein. Eng. 7(9), 1059-1068 (1994)
    • (1994) Protein. Eng , vol.7 , Issue.9 , pp. 1059-1068
    • Lathrop, R.H.1
  • 31
    • 0029912991 scopus 로고    scopus 로고
    • Global optimum protein threading with gapped alignment and empirical pair score functions
    • Lathrop, R.H., Smith, T.F.: Global optimum protein threading with gapped alignment and empirical pair score functions. J. Mol. Biol. 255(4), 641-665 (1996)
    • (1996) J. Mol. Biol , vol.255 , Issue.4 , pp. 641-665
    • Lathrop, R.H.1    Smith, T.F.2
  • 32
    • 0024750637 scopus 로고
    • A lattice statistical mechanics model of the conformational and sequence spaces of proteins
    • Lau, K.E, Dill, K.A.: A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Journal of the American Chemical Society 22 (1989)
    • (1989) Journal of the American Chemical Society , vol.22
    • Lau, K.E.1    Dill, K.A.2
  • 34
    • 38149058322 scopus 로고    scopus 로고
    • Michel, L., See, A., Van Hentenryck, P.: Parallelizing Constraint Programs Transparently. In: Bessière, C. (ed.) CP 2007. LNCS, 4741, pp. 514-528. Springer, Heidelberg (2007)
    • Michel, L., See, A., Van Hentenryck, P.: Parallelizing Constraint Programs Transparently. In: Bessière, C. (ed.) CP 2007. LNCS, vol. 4741, pp. 514-528. Springer, Heidelberg (2007)
  • 35
    • 0032960853 scopus 로고    scopus 로고
    • Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues
    • Miyazawa, S., Jernigan, R.L.: Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues. Proteins 34(1) (1999)
    • (1999) Proteins , vol.34 , Issue.1
    • Miyazawa, S.1    Jernigan, R.L.2
  • 37
  • 38
    • 56449096565 scopus 로고    scopus 로고
    • Shaw, P.: Using Constraint Programming and Local Search Methods to Solve Vehicle Routing Problems. In: Maher, M.J., Puget, J.-F. (eds.) CP 1998. LNCS, 1520. Springer, Heidelberg (1998)
    • Shaw, P.: Using Constraint Programming and Local Search Methods to Solve Vehicle Routing Problems. In: Maher, M.J., Puget, J.-F. (eds.) CP 1998. LNCS, vol. 1520. Springer, Heidelberg (1998)
  • 39
    • 0034958379 scopus 로고    scopus 로고
    • Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP
    • Siew, N., Fischer, D.: Convergent evolution of protein structure prediction and computer chess tournaments: CASP, Kasparov, and CAFASP. IBM Systems Journal 40(2) (2001)
    • (2001) IBM Systems Journal , vol.40 , Issue.2
    • Siew, N.1    Fischer, D.2
  • 40
    • 0025341310 scopus 로고
    • Calculation of conformation ensembles from potentials of mean force
    • Sippl, M.: Calculation of conformation ensembles from potentials of mean force. J. Mol. Biol. 213, 859-883(1990)
    • (1990) J. Mol. Biol , vol.213 , pp. 859-883
    • Sippl, M.1
  • 41
    • 0025608908 scopus 로고
    • Simulations of the Folding of a Globular
    • Skolnick, J., Kolinski, A.: Simulations of the Folding of a Globular Protein. Science 250(4984), 1121-1125 (1990)
    • (1990) Protein. Science , vol.250 , Issue.4984 , pp. 1121-1125
    • Skolnick, J.1    Kolinski, A.2
  • 42
    • 0023991155 scopus 로고
    • The effect of amino acid substitution on protein-folding and -unfolding transition studied by computer simulation
    • Taketomi, H., Kano, F, Go, N.: The effect of amino acid substitution on protein-folding and -unfolding transition studied by computer simulation. Biopolymers 27(4) (1988)
    • (1988) Biopolymers , vol.27 , Issue.4
    • Taketomi, H.1    Kano, F.2    Go, N.3
  • 43
    • 0027245418 scopus 로고
    • Genetic algorithms for protein folding simulations
    • Unger, R., Moult, J.: Genetic algorithms for protein folding simulations. Journal of Molecular Biology 231, 75-81 (1993)
    • (1993) Journal of Molecular Biology , vol.231 , pp. 75-81
    • Unger, R.1    Moult, J.2
  • 45
    • 0036366692 scopus 로고    scopus 로고
    • Constraint-based hydrophobic core construction for protein structure prediction in the face-centered-cubic lattice
    • Will, S.: Constraint-based hydrophobic core construction for protein structure prediction in the face-centered-cubic lattice. In: Pacific Symposium on Biocomputing (2002)
    • (2002) Pacific Symposium on Biocomputing
    • Will, S.1
  • 46
    • 56449104617 scopus 로고    scopus 로고
    • Will, S.: Exact, Constraint-Based Structure Prediction in Simple Protein Models. In: PhD thesis, Friedrich-Schiller-Universität Jena (April 2005)
    • Will, S.: Exact, Constraint-Based Structure Prediction in Simple Protein Models. In: PhD thesis, Friedrich-Schiller-Universität Jena (April 2005)
  • 47
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • Wu, S., Skolnick, J., Zhang, Y: Ab initio modeling of small proteins by iterative TASSER simulations. BMC. Biol. 5, 17 (2007)
    • (2007) BMC. Biol , vol.5 , pp. 17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 48
    • 0030048675 scopus 로고    scopus 로고
    • Folding proteins with a simple energy function and extensive conformational searching
    • Yue, K., Dill, K.A.: Folding proteins with a simple energy function and extensive conformational searching. Protein. Sci. 5(2), 254-261 (1996)
    • (1996) Protein. Sci , vol.5 , Issue.2 , pp. 254-261
    • Yue, K.1    Dill, K.A.2
  • 51
    • 39449115394 scopus 로고    scopus 로고
    • structure prediction. Bioinformatics
    • Zhang, Y.: I-TASSER server for protein 3D structure prediction. Bioinformatics (2008)
    • (2008) I-TASSER server for protein , vol.3 D
    • Zhang, Y.1
  • 52
    • 12844288890 scopus 로고    scopus 로고
    • The protein structure prediction problem could be solved using the current PDB library
    • Zhang, Y.;, Skolnick, J.: The protein structure prediction problem could be solved using the current PDB library. Proc. Natl. Acad. Sci. U.S.A. 102(4), 1029-1034 (2005)
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , Issue.4 , pp. 1029-1034
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.