메뉴 건너뛰기




Volumn 4, Issue 2, 2006, Pages 91-123

Some operations research methods for analyzing protein sequences and structures

Author keywords

Clustering; Dynamic programming; Hidden Markov model; Neural networks; Protein structure

Indexed keywords


EID: 33746095828     PISSN: 16194500     EISSN: 16142411     Source Type: Journal    
DOI: 10.1007/s10288-006-0089-y     Document Type: Article
Times cited : (11)

References (155)
  • 4
    • 10044297099 scopus 로고    scopus 로고
    • Protein threading: From mathematical models to parallel implementations
    • Andonov R, Balev S, Yanev N (2004) Protein threading: From mathematical models to parallel implementations. INFORMS Journal on Computing, 16(4)
    • (2004) INFORMS Journal on Computing , vol.16 , Issue.4
    • Andonov, R.1    Balev, S.2    Yanev, N.3
  • 5
    • 0030633417 scopus 로고    scopus 로고
    • Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system
    • (Gaasterland, T., Karp, P., Karplus, K., Ouzounis, C., Sander, C. et al., eds.), AAAI Press, Halkidiki, Greece
    • Andrade MA, Valencia A (1997) Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system. In Fifth International Conference on Intelligent Systems for Molecular Biology (Gaasterland, T., Karp, P., Karplus, K., Ouzounis, C., Sander, C. et al., eds.), AAAI Press, Halkidiki, Greece, pp. 25-32
    • (1997) Fifth International Conference on Intelligent Systems for Molecular Biology , pp. 25-32
    • Andrade, M.A.1    Valencia, A.2
  • 7
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181: 223-230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 8
    • 67349189383 scopus 로고
    • The kynetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain
    • Anfinsen CB, Haber E, Sela M, White Jr F (1961) The kynetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. PNAS 47(9): 1309-1314
    • (1961) PNAS , vol.47 , Issue.9 , pp. 1309-1314
    • Anfinsen, C.B.1    Haber, E.2    Sela, M.3    White Jr., F.4
  • 11
    • 0027174134 scopus 로고
    • Prediction of protein secondary structure by the hidden Markov model
    • Asai K, Hayamizu S, Handa K (1993) Prediction of protein secondary structure by the hidden Markov model. Bioinformatics 9: 141-146
    • (1993) Bioinformatics , vol.9 , pp. 141-146
    • Asai, K.1    Hayamizu, S.2    Handa, K.3
  • 12
    • 0033986922 scopus 로고    scopus 로고
    • The quest to deduce protein function from sequence: The role of pattern databases
    • Attwood TK (2000) The quest to deduce protein function from sequence: The role of pattern databases. Int. J. Biochem. Cell. Biol., 32: 139-155
    • (2000) Int. J. Biochem. Cell. Biol. , vol.32 , pp. 139-155
    • Attwood, T.K.1
  • 14
    • 0033957834 scopus 로고    scopus 로고
    • The S WISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch A, Apweiler R (2000) The S WISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research, 28: 45-48
    • (2000) Nucleic Acids Research , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 16
    • 0033369033 scopus 로고    scopus 로고
    • Exploiting the past and the future in protein secondary structure prediction
    • Baldi P, Brunak S, Frasconi P, Soda G, Pollastri G (1999) Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15: 937-946
    • (1999) Bioinformatics , vol.15 , pp. 937-946
    • Baldi, P.1    Brunak, S.2    Frasconi, P.3    Soda, G.4    Pollastri, G.5
  • 18
    • 25144463996 scopus 로고    scopus 로고
    • Optimal protein structure alignment using maximum cliques
    • Barnes E, Sokol JS, Strickland DM (2005) Optimal protein structure alignment using maximum cliques. Operations Research, 53:389-402
    • (2005) Operations Research , vol.53 , pp. 389-402
    • Barnes, E.1    Sokol, J.S.2    Strickland, D.M.3
  • 20
    • 0000342467 scopus 로고
    • Statistical inference for probabilistic functions of finite state Markov chains
    • Baum LE, Petrie T (1966) Statistical inference for probabilistic functions of finite state Markov chains. Annals of Mathematical Statistics Vol. 37
    • (1966) Annals of Mathematical Statistics , vol.37
    • Baum, L.E.1    Petrie, T.2
  • 21
    • 0025935158 scopus 로고
    • Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure of the catalytic domain of protein kinases
    • Benner SA, Gerloff D (1990) Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure of the catalytic domain of protein kinases. Adv. Enz. Reg. 31: 121-181
    • (1990) Adv. Enz. Reg. , vol.31 , pp. 121-181
    • Benner, S.A.1    Gerloff, D.2
  • 27
    • 0343638829 scopus 로고    scopus 로고
    • Selected combinatorial optimization problemsarising in molecular biology
    • Blażewicz J, Kasprzak M, Sterna M, Wêglarz J (1997) Selected combinatorial optimization problemsarising in molecular biology. Ricerca Operativa 26: 35-63
    • (1997) Ricerca Operativa , vol.26 , pp. 35-63
    • Blazewicz, J.1    Kasprzak, M.2    Sterna, M.3    Wêglarz, J.4
  • 28
    • 24144487043 scopus 로고    scopus 로고
    • Application of tabu search strategy for finding low energy structure of protein
    • Blażewicz J, Lukasiak P, Milostan M (2005b) Application of tabu search strategy for finding low energy structure of protein. Artificial Intelligence in Medicine 35(1-2): 135-145
    • (2005) Artificial Intelligence in Medicine , vol.35 , Issue.1-2 , pp. 135-145
    • Blazewicz, J.1    Lukasiak, P.2    Milostan, M.3
  • 30
    • 0029846866 scopus 로고    scopus 로고
    • Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks
    • Blom N, Hansen J, Blaas D, Brunak S (1996) Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks. Prot. Sci. 5: 2203-2216
    • (1996) Prot. Sci. , vol.5 , pp. 2203-2216
    • Blom, N.1    Hansen, J.2    Blaas, D.3    Brunak, S.4
  • 32
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-170
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 33
  • 35
    • 0008414949 scopus 로고
    • Non-linearities in training sets identified by inspecting the order in which neural networks learn
    • (Benhar, O., Bosio, C., Del Giudice, P. & Tabet, E., eds.), Elba, Italy
    • Brunak S (1991) Non-linearities in training sets identified by inspecting the order in which neural networks learn. In Neural Networks From Biology to High Energy Physics (Benhar, O., Bosio, C., Del Giudice, P. & Tabet, E., eds.), Elba, Italy, pp 277-88
    • (1991) Neural Networks from Biology to High Energy Physics , pp. 277-288
    • Brunak, S.1
  • 36
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • Bystroff C, Baker D (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of Molecular Biology 281: 565-577
    • (1998) Journal of Molecular Biology , vol.281 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 37
    • 0034604368 scopus 로고    scopus 로고
    • HMMSTR: A hidden markov model for local sequence-structure correlations in proteins
    • Bystroff C, Thorsson V, Baker D (2000) HMMSTR: A hidden markov model for local sequence-structure correlations in proteins. Journal of Molecular Biology 301: 173-90
    • (2000) Journal of Molecular Biology , vol.301 , pp. 173-190
    • Bystroff, C.1    Thorsson, V.2    Baker, D.3
  • 38
    • 1842451398 scopus 로고    scopus 로고
    • 1001 Optimal pdb structure alignments: Integer programming methods for finding the maximum contact map overlap
    • Caprara A, Carr B, Istrail S, Lancia G, Walenz B (2004) 1001 optimal pdb structure alignments: Integer programming methods for finding the maximum contact map overlap. Journal of Computational Biology, 11(1):27-52
    • (2004) Journal of Computational Biology , vol.11 , Issue.1 , pp. 27-52
    • Caprara, A.1    Carr, B.2    Istrail, S.3    Lancia, G.4    Walenz, B.5
  • 40
    • 29044441607 scopus 로고    scopus 로고
    • Compact optimization can outperform separation: A case study in structural proteomics
    • Carr RD, Lancia G (2004) Compact optimization can outperform separation: a case study in structural proteomics. 4OR, 2(3):221-233
    • (2004) 4OR , vol.2 , Issue.3 , pp. 221-233
    • Carr, R.D.1    Lancia, G.2
  • 41
    • 0141963801 scopus 로고    scopus 로고
    • The side-chain positioning problem: A semidefinite programming formulation with new rounding schemes
    • Paris C. Kanellakis Memorial Workshop. ACM Press
    • Chazelle B, Kingsford C, Singh M (2003) The side-chain positioning problem: A semidefinite programming formulation with new rounding schemes. In PCK50 - Principles of Computing & Knowledge, Paris C. Kanellakis Memorial Workshop, pages 86-94. ACM Press
    • (2003) PCK50 - Principles of Computing & Knowledge , pp. 86-94
    • Chazelle, B.1    Kingsford, C.2    Singh, M.3
  • 42
    • 10044241588 scopus 로고    scopus 로고
    • A semidefinite programming approach to side chain positioning with new rounding strategies
    • Chazelle B, Kingsford C, Singh M (2004) A semidefinite programming approach to side chain positioning with new rounding strategies. INFORMS Journal on Computing, 16(4)
    • (2004) INFORMS Journal on Computing , vol.16 , Issue.4
    • Chazelle, B.1    Kingsford, C.2    Singh, M.3
  • 43
    • 0033957841 scopus 로고    scopus 로고
    • ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
    • Corpet F, Servant F, Gouzy J, Kahn D (2000) ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons. Nucleic Acids Research, 28: 267-269
    • (2000) Nucleic Acids Research , vol.28 , pp. 267-269
    • Corpet, F.1    Servant, F.2    Gouzy, J.3    Kahn, D.4
  • 44
    • 0033106244 scopus 로고    scopus 로고
    • Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
    • Cuff JA, Barton GJ (1999) Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 34: 508-519
    • (1999) Proteins , vol.34 , pp. 508-519
    • Cuff, J.A.1    Barton, G.J.2
  • 48
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 49
    • 0035953487 scopus 로고    scopus 로고
    • Role and results of statistical methods in protein fold class prediction
    • Edler L, Grassmann J, Suhai S (2001) Role and results of statistical methods in protein fold class prediction. Mathematical and ComputerModelling 33: 1401-1417
    • (2001) Mathematical and ComputerModelling , vol.33 , pp. 1401-1417
    • Edler, L.1    Grassmann, J.2    Suhai, S.3
  • 50
    • 0030910802 scopus 로고    scopus 로고
    • Structural trees for protein superfamilies
    • Efimov AV (1997) Structural trees for protein superfamilies. Proteins 28: 241-260
    • (1997) Proteins , vol.28 , pp. 241-260
    • Efimov, A.V.1
  • 51
    • 68549106477 scopus 로고    scopus 로고
    • Side chain-positioning as an integer programming problem
    • O. Gascuel and B. M. E. Moret, editors, Proceedings of AnnualWorkshop on Algorithms in Bioinformatics (WABI), Springer
    • Eriksson O, Zhou Y, Elofsson A (2001) Side chain-positioning as an integer programming problem. In O. Gascuel and B. M. E. Moret, editors, Proceedings of AnnualWorkshop on Algorithms in Bioinformatics (WABI), volume 2149 of Lecture Notes in Computer Science, pp 128-141, Springer
    • (2001) Lecture Notes in Computer Science , vol.2149 , pp. 128-141
    • Eriksson, O.1    Zhou, Y.2    Elofsson, A.3
  • 53
    • 0032588985 scopus 로고    scopus 로고
    • Prediction of protein tertiary structure to low resolution: Performance for a large and structurally diverse test set
    • Eyrich VA, Standley DM, Friesner RA (1999) Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set. Journal of Molecular Biology 288(4): 725-742
    • (1999) Journal of Molecular Biology , vol.288 , Issue.4 , pp. 725-742
    • Eyrich, V.A.1    Standley, D.M.2    Friesner, R.A.3
  • 54
    • 0027764341 scopus 로고
    • A hybrid method to cluster protein sequences based on statistics and artificial neural networks
    • Ferrán EA, Pflugfelder B (1993) A hybrid method to cluster protein sequences based on statistics and artificial neural networks. CABIOS 9: 671-680
    • (1993) CABIOS , vol.9 , pp. 671-680
    • Ferrán, E.A.1    Pflugfelder, B.2
  • 56
    • 0023479421 scopus 로고
    • Why do globular proteins fit the limited set of folding patterns?
    • Finkelstein AV, Ptitsyn OB (1987) Why do globular proteins fit the limited set of folding patterns? Prog. Biophys. Mol. Biol. 50: 171-190
    • (1987) Prog. Biophys. Mol. Biol. , vol.50 , pp. 171-190
    • Finkelstein, A.V.1    Ptitsyn, O.B.2
  • 58
    • 0027070916 scopus 로고
    • Recognition of distantly related protein sequences using conserved motifs and neural networks
    • Frishman D, Argos P (1992) Recognition of distantly related protein sequences using conserved motifs and neural networks. Journal of Molecular Biology 228: 951-962
    • (1992) Journal of Molecular Biology , vol.228 , pp. 951-962
    • Frishman, D.1    Argos, P.2
  • 59
    • 0026726481 scopus 로고
    • Topology fingerprint approach to the inverse protein folding problem
    • Godzik A, Skolnick J, Kolinski A (1992) Topology fingerprint approach to the inverse protein folding problem. Journal of Molecular Biology 227: 227-238
    • (1992) Journal of Molecular Biology , vol.227 , pp. 227-238
    • Godzik, A.1    Skolnick, J.2    Kolinski, A.3
  • 60
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough J, Karplus K, Hughey R, Chothia C (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. Journal of Molecular Biology, 313: 903-919
    • (2001) Journal of Molecular Biology , vol.313 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 61
    • 4544326903 scopus 로고    scopus 로고
    • Opportunities for combinatorial optimization in computational biology
    • Greenberg H, Hart W, Lancia G (2004) Opportunities for combinatorial optimization in computational biology. INFORMS Journal on Computing, 16(3): 1-22
    • (2004) INFORMS Journal on Computing , vol.16 , Issue.3 , pp. 1-22
    • Greenberg, H.1    Hart, W.2    Lancia, G.3
  • 63
    • 0033200307 scopus 로고    scopus 로고
    • A systematic comparison of protein structure classifications: SCOP, CATH and FSSP
    • Hadley C, Jones DT (1999) A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure 7: 1099-1112
    • (1999) Structure , vol.7 , pp. 1099-1112
    • Hadley, C.1    Jones, D.T.2
  • 64
    • 0029898244 scopus 로고    scopus 로고
    • Global properties of the mapping between local amino acid sequence and local structure in proteins
    • Han KF, Baker D (1996) Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc. Natl Acad. Sci. USA 93: 5814-5818
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 5814-5818
    • Han, K.F.1    Baker, D.2
  • 65
    • 0031809552 scopus 로고    scopus 로고
    • NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility
    • Hansen JE, Lund O, Tolstrup N, Gooley AA, Williams KL, Brunak S (1998) NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glyconjug. J. 15: 115-130
    • (1998) Glyconjug. J. , vol.15 , pp. 115-130
    • Hansen, J.E.1    Lund, O.2    Tolstrup, N.3    Gooley, A.A.4    Williams, K.L.5    Brunak, S.6
  • 68
    • 0025816343 scopus 로고
    • Prediction of ATP-binding motifs a comparison of a perceptron-type neural network and a consensus sequence method
    • Hirst JD, Sternberg MJE (1991) Prediction of ATP-binding motifs a comparison of a perceptron-type neural network and a consensus sequence method. Protein Engineering 4: 615-623
    • (1991) Protein Engineering , vol.4 , pp. 615-623
    • Hirst, J.D.1    Sternberg, M.J.E.2
  • 69
    • 0026672260 scopus 로고
    • Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks
    • Hirst JD, Sternberg MJE (1992) Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks. Biochem. 31: 615-623
    • (1992) Biochem. , vol.31 , pp. 615-623
    • Hirst, J.D.1    Sternberg, M.J.E.2
  • 71
    • 0000268209 scopus 로고
    • Protein Secondary Structure Prediction with a Neural Network
    • Holley H, Karplus M (1989) Protein Secondary Structure Prediction with a Neural Network. Proc. Natl Acad. Sci. USA 86: 152-156
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 152-156
    • Holley, H.1    Karplus, M.2
  • 72
    • 0027440362 scopus 로고
    • Protein structures comparision by alignment of distance matrices
    • Holm L, Sander C (1993) Protein structures comparision by alignment of distance matrices. Journal of Molecular Biology 233: 123-138
    • (1993) Journal of Molecular Biology , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 73
    • 0027991446 scopus 로고
    • The FSSP database of structurally aligned protein fold families
    • Holm L, Sander C (1994) The FSSP database of structurally aligned protein fold families. Nucleic Acids Research 22: 3600-3609
    • (1994) Nucleic Acids Research , vol.22 , pp. 3600-3609
    • Holm, L.1    Sander, C.2
  • 74
    • 0030765455 scopus 로고    scopus 로고
    • Dali/FSSP classification of three-dimensional protein folds
    • Holm L, Sander C (1997) Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Research 25: 231-234
    • (1997) Nucleic Acids Research , vol.25 , pp. 231-234
    • Holm, L.1    Sander, C.2
  • 75
    • 0035957531 scopus 로고    scopus 로고
    • A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach
    • Hua S, Sun Z (2001) A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach. Journal of Molecular Biology 308: 397-407
    • (2001) Journal of Molecular Biology , vol.308 , pp. 397-407
    • Hua, S.1    Sun, Z.2
  • 76
    • 0034119780 scopus 로고    scopus 로고
    • Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites
    • Jagla B, Schuchhardt J (2000) Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites. Bioinformatics, 16: 245-250
    • (2000) Bioinformatics , vol.16 , pp. 245-250
    • Jagla, B.1    Schuchhardt, J.2
  • 77
    • 0014129195 scopus 로고
    • Hierarchical clustering schemes
    • Johnson SC (1967) Hierarchical clustering schemes. Psychometrika 32: 241-254
    • (1967) Psychometrika , vol.32 , pp. 241-254
    • Johnson, S.C.1
  • 78
    • 0010757239 scopus 로고
    • This week's citation classic
    • Johnson SC (1985) This week's citation classic. Current Contents 5: 16
    • (1985) Current Contents , vol.5 , pp. 16
    • Johnson, S.C.1
  • 79
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292: 195-202
    • (1999) Journal of Molecular Biology , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 80
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones DT (1999a) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. Journal of Molecular Biology 287: 797-815
    • (1999) Journal of Molecular Biology , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 81
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM (1992) A new approach to protein fold recognition. Nature 358: 86-89
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 84
    • 0025334980 scopus 로고
    • Improvements in protein secondary structure prediction by an enhanced neural network
    • Kneller D, Cohen F, Langridge R (1990) Improvements in protein secondary structure prediction by an enhanced neural network. Journal of Molecular Biology 214: 171-182
    • (1990) Journal of Molecular Biology , vol.214 , pp. 171-182
    • Kneller, D.1    Cohen, F.2    Langridge, R.3
  • 85
    • 0142184275 scopus 로고    scopus 로고
    • PROSPECT II: Protein structure prediction program for genome-scale applications
    • Kim D, Xu D, Guo J, Ellrott K, Xu Y (2003) PROSPECT II: protein structure prediction program for genome-scale applications. Protein Engineering 16(9): 641-650
    • (2003) Protein Engineering , vol.16 , Issue.9 , pp. 641-650
    • Kim, D.1    Xu, D.2    Guo, J.3    Ellrott, K.4    Xu, Y.5
  • 86
    • 16344382546 scopus 로고    scopus 로고
    • Solving and analyzing side-chain positioning problems using linear and integer programming
    • Kingsford C, Chazelle B, Singh M (2005) Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics, 21(7):1028-1039
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 1028-1039
    • Kingsford, C.1    Chazelle, B.2    Singh, M.3
  • 88
    • 0020068152 scopus 로고
    • Self-organized formation of topologically correct feature maps
    • Kohonen T (1982) Self-organized formation of topologically correct feature maps. Biol. Cybern. 43: 59-69
    • (1982) Biol. Cybern. , vol.43 , pp. 59-69
    • Kohonen, T.1
  • 90
    • 0347753603 scopus 로고    scopus 로고
    • Reduced models of proteins and their applications
    • Kolinski A, Skolnick J (2004a) Reduced models of proteins and their applications. Polymer 45: 511-524
    • (2004) Polymer , vol.45 , pp. 511-524
    • Kolinski, A.1    Skolnick, J.2
  • 92
    • 0025945726 scopus 로고
    • Improving signal peptide prediction accuracy by simulated neural network
    • Ladunga I, Czakó F, Csabai I, Geszti T (1991) Improving signal peptide prediction accuracy by simulated neural network. CABIOS 7: 485-487
    • (1991) CABIOS , vol.7 , pp. 485-487
    • Ladunga, I.1    Czakó, F.2    Csabai, I.3    Geszti, T.4
  • 94
    • 0028015988 scopus 로고
    • The protein threading problem with sequence amino acid interaction preferences is NP-complete
    • Lathrop RH (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Engineering 7: 1059-1068
    • (1994) Protein Engineering , vol.7 , pp. 1059-1068
    • Lathrop, R.H.1
  • 96
    • 0002006297 scopus 로고
    • Are there pathways to protein folding ?
    • Levinthal C (1968) Are there pathways to protein folding ? J. Chem. Phys. 65: 44-45
    • (1968) J. Chem. Phys. , vol.65 , pp. 44-45
    • Levinthal, C.1
  • 97
    • 17444405333 scopus 로고    scopus 로고
    • Hidden Markov models with states depending on observations
    • Lee Y (2005) Hidden Markov models with states depending on observations. Pattern Recognition Letters, 26: 977-984
    • (2005) Pattern Recognition Letters , vol.26 , pp. 977-984
    • Lee, Y.1
  • 98
    • 0036169928 scopus 로고    scopus 로고
    • Tolerating some redundancy significantly speeds up clustering of large protein databases
    • Li W, Jaroszewski L, Godzik A (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics, 18: 77-82
    • (2002) Bioinformatics , vol.18 , pp. 77-82
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 99
    • 0037305939 scopus 로고    scopus 로고
    • Domains, motifs and clusters in protein universe
    • 2003
    • Liu J, Rost B (2003) Domains, motifs and clusters in protein universe. Current Opinion in Chemical Biology, 2003 7: 5-11
    • (2003) Current Opinion in Chemical Biology , vol.7 , pp. 5-11
    • Liu, J.1    Rost, B.2
  • 100
    • 0034695414 scopus 로고    scopus 로고
    • Identification of related proteins on family, superfamily and fold level
    • Lindahl E, Elofsson A (2000) Identification of related proteins on family, superfamily and fold level. Journal of Molecular Biology 295: 613-625
    • (2000) Journal of Molecular Biology , vol.295 , pp. 613-625
    • Lindahl, E.1    Elofsson, A.2
  • 101
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman DJ, Pearson WR (1985) Rapid and sensitive protein similarity searches. Science, 227: 1435-1441
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 103
    • 27644494405 scopus 로고    scopus 로고
    • Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks
    • Ma Q, Chirn G-W, Cai R, Szustakowski J, Nirmala NR (2005) Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks. Bioinformatics 6: 242
    • (2005) Bioinformatics , vol.6 , pp. 242
    • Ma, Q.1    Chirn, G.-W.2    Cai, R.3    Szustakowski, J.4    Nirmala, N.R.5
  • 104
    • 0038062969 scopus 로고    scopus 로고
    • Support vector machines for protein fold class prediction
    • Markowetz F, Edler L, Vingron M (2003) Support vector machines for protein fold class prediction. Biometrical Journal 45(3): 377-389
    • (2003) Biometrical Journal , vol.45 , Issue.3 , pp. 377-389
    • Markowetz, F.1    Edler, L.2    Vingron, M.3
  • 106
    • 0031766401 scopus 로고    scopus 로고
    • HOMSTRAD: A database of protein structure alignments for homologous families
    • Mizuguchi K, Deane CM, Blundell TL, Overington JP (1998) HOMSTRAD: A database of protein structure alignments for homologous families. Protein Sci. 7: 2469-2471
    • (1998) Protein Sci. , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3    Overington, J.P.4
  • 107
    • 4444270864 scopus 로고    scopus 로고
    • Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques
    • Mohseni-Zadeh S, Brzellec P, Risler J-L (2004) Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques. Computational Biology and Chemistry 28(3): 211-218
    • (2004) Computational Biology and Chemistry , vol.28 , Issue.3 , pp. 211-218
    • Mohseni-Zadeh, S.1    Brzellec, P.2    Risler, J.-L.3
  • 108
    • 0033985048 scopus 로고    scopus 로고
    • The SBASE protein domain library, release 7.0: A collection of annotated protein sequence segments
    • Murvai J, Vlahovicek K, Barta E, Cataletto B, Pongor S (2000) The SBASE protein domain library, release 7.0: A collection of annotated protein sequence segments. Nucleic Acids Research, 28: 260-262
    • (2000) Nucleic Acids Research , vol.28 , pp. 260-262
    • Murvai, J.1    Vlahovicek, K.2    Barta, E.3    Cataletto, B.4    Pongor, S.5
  • 109
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 247: 536-540
    • (1995) Journal of Molecular Biology , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 110
    • 25644455245 scopus 로고    scopus 로고
    • Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA and CFMC
    • Nanias M, Chinchio M, O'dziej S, Czaplewski C, Scheraga HA (2005) Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA and CFMC. J. Comput. Chem., 26: 1472-1486
    • (2005) J. Comput. Chem. , vol.26 , pp. 1472-1486
    • Nanias, M.1    Chinchio, M.2    O'Dziej, S.3    Czaplewski, C.4    Scheraga, H.A.5
  • 111
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequences of two proteins
    • Needleman S, Wunsch, C (1970) A general method applicable to the search for similarities in the amino acid sequences of two proteins. Journal of Molecular Biology 48: 443-453
    • (1970) Journal of Molecular Biology , vol.48 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 112
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen H, Engelbrecht J, Brunak S, von Heijne G (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering 10: 1-6
    • (1997) Protein Engineering , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    Von Heijne, G.4
  • 113
    • 0025604880 scopus 로고
    • Improving the prediction of secondary structure of TIM-barrel' enzymes
    • Niermann T, Kirschner K (1990) Improving the prediction of secondary structure of TIM-barrel' enzymes. Protein Engineering 4: 137-147
    • (1990) Protein Engineering , vol.4 , pp. 137-147
    • Niermann, T.1    Kirschner, K.2
  • 115
    • 0033933636 scopus 로고    scopus 로고
    • Cascaded multiple classifiers for secondary structure prediction
    • Ouali M, King RD (2000) Cascaded multiple classifiers for secondary structure prediction. Protein Sci. 9: 1162-1176
    • (2000) Protein Sci. , vol.9 , pp. 1162-1176
    • Ouali, M.1    King, R.D.2
  • 118
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA, 85: 2444-2448
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 121
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • Pollastri G, Przybylski D, Rost B, Baldi P (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47: 228-235
    • (2002) Proteins , vol.47 , pp. 228-235
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 122
    • 0041719954 scopus 로고    scopus 로고
    • Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
    • Pollastri G, Baldi P (2002) Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics 18(1): S62-S70
    • (2002) Bioinformatics , vol.18 , Issue.1
    • Pollastri, G.1    Baldi, P.2
  • 123
    • 0036467068 scopus 로고    scopus 로고
    • Alignments grow, secondary structure prediction improves
    • Przybylski D, Rost B (2002) Alignments grow, secondary structure prediction improves. Proteins 46: 197-205
    • (2002) Proteins , vol.46 , pp. 197-205
    • Przybylski, D.1    Rost, B.2
  • 124
    • 0019053499 scopus 로고
    • Similarities of protein topologies: Evolutionary divergence, functional convergence or principles of folding?
    • Ptitsyn OB, Finkelstein AV (1980) Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding? Q. Rev. Biophys. 13: 339-386
    • (1980) Q. Rev. Biophys. , vol.13 , pp. 339-386
    • Ptitsyn, O.B.1    Finkelstein, A.V.2
  • 125
    • 0023803244 scopus 로고
    • Predicting the secondary structure of globular proteins using neural network models
    • Qian N, Sejnowski T (1988) Predicting the secondary structure of globular proteins using neural network models. Journal of Molecular Biology 202: 865-884
    • (1988) Journal of Molecular Biology , vol.202 , pp. 865-884
    • Qian, N.1    Sejnowski, T.2
  • 126
    • 0024610919 scopus 로고
    • A tutorial on hidden markov models and selected applications in speech recognition
    • Rabiner LR (1989) A tutorial on hidden markov models and selected applications in speech recognition. Proceedings of the IEEE 77(2): 257-286
    • (1989) Proceedings of the IEEE , vol.77 , Issue.2 , pp. 257-286
    • Rabiner, L.R.1
  • 127
    • 0029984070 scopus 로고    scopus 로고
    • Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments
    • Riis SK, Krogh A (1996) Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments. J. Comput. Biol. 3: 163-183
    • (1996) J. Comput. Biol. , vol.3 , pp. 163-183
    • Riis, S.K.1    Krogh, A.2
  • 128
    • 0027169638 scopus 로고
    • Improved prediction of protein secondary structure by use of sequence profiles and neural networks
    • Rost B, Sander C (1993a) Improved Prediction of Protein Secondary Structure by Use of Sequence Profiles and Neural Networks. Proc. Natl Acad. Sci. USA 90: 7558-7562
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 7558-7562
    • Rost, B.1    Sander, C.2
  • 129
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost B, Sander C (1993b) Prediction of protein secondary structure at better than 70% accuracy. Journal of Molecular Biology 232: 584-599
    • (1993) Journal of Molecular Biology , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 130
    • 0028158628 scopus 로고
    • PHD - An automatic server for protein secondary structure prediction
    • Rost B, Sander C, Schneider R (1994) PHD - an automatic server for protein secondary structure prediction. CABIOS 10: 53-60
    • (1994) CABIOS , vol.10 , pp. 53-60
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 132
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski L, Jaroszewski L, Li W, Godzik A (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 9: 232-241
    • (2000) Protein Sci. , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 133
    • 0027233815 scopus 로고
    • Development of artificial neural filters for pattern recognition in protein sequences
    • Schneider G, Wrede P (1993) Development of artificial neural filters for pattern recognition in protein sequences. J. Mol. Evol. 36: 586-595
    • (1993) J. Mol. Evol. , vol.36 , pp. 586-595
    • Schneider, G.1    Wrede, P.2
  • 135
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi J, Blundell TL, Mizuguchi K (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. Journal of Molecular Biology 310: 243-257
    • (2001) Journal of Molecular Biology , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 138
    • 0033963523 scopus 로고    scopus 로고
    • Searching for the ideal forms of proteins
    • Taylor WR (2000) Searching for the ideal forms of proteins. Biochem. Soc. Trans. 28: 264-269
    • (2000) Biochem. Soc. Trans. , vol.28 , pp. 264-269
    • Taylor, W.R.1
  • 139
    • 1442315781 scopus 로고    scopus 로고
    • Mewes,B. and Weiss,H.S. (eds). Springer-Verlag, Berlin, Ernst Schering Research Foundation Workshop
    • Taylor WR (2002a) In Mewes,B. and Weiss,H.S. (eds), Bioinformatics and Genome Analysis. Springer-Verlag, Berlin, Ernst Schering Research Foundation Workshop Vol. 38, pp 133-148
    • (2002) Bioinformatics and Genome Analysis , vol.38 , pp. 133-148
    • Taylor, W.R.1
  • 140
    • 0037061460 scopus 로고    scopus 로고
    • A 'periodic table' for protein structures
    • Taylor WR (2002b) A 'periodic table' for protein structures. Nature 416: 657-660
    • (2002) Nature , vol.416 , pp. 657-660
    • Taylor, W.R.1
  • 142
    • 0028081516 scopus 로고
    • Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies
    • Tolstrup N, Toftgård J, Engelbrecht J, Brunak S (1994) Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies. Journal of Molecular Biology 243: 816-820
    • (1994) Journal of Molecular Biology , vol.243 , pp. 816-820
    • Tolstrup, N.1    Toftgård, J.2    Engelbrecht, J.3    Brunak, S.4
  • 143
    • 0036267995 scopus 로고    scopus 로고
    • Hidden Markov Models-based system (HMMSPECTR) for detecting structural homologies on the basis of sequential information
    • Tsigelny I, Sharikov Y, Ten Eyck LF (2002) Hidden Markov Models-based system (HMMSPECTR) for detecting structural homologies on the basis of sequential information, Protein Engineering 15(5): 347-352
    • (2002) Protein Engineering , vol.15 , Issue.5 , pp. 347-352
    • Tsigelny, I.1    Sharikov, Y.2    Ten Eyck, L.F.3
  • 145
    • 1842857770 scopus 로고    scopus 로고
    • Large-scale linear programming techniques for the design of protein folding potentials
    • Wagner M, Meller J, Elber R (2004) Large-scale linear programming techniques for the design of protein folding potentials. Mathematical Programming, 101(2):301-318
    • (2004) Mathematical Programming , vol.101 , Issue.2 , pp. 301-318
    • Wagner, M.1    Meller, J.2    Elber, R.3
  • 147
    • 0020714456 scopus 로고
    • Rapid similarity searches of nucleic acid and protein data banks
    • Wilbur WJ, Lipman DJ (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. USA, 80: 726-730
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 726-730
    • Wilbur, W.J.1    Lipman, D.J.2
  • 148
    • 0029933832 scopus 로고    scopus 로고
    • Motif identification neural design for rapid and sensitive protein family search
    • Wu CH, Zhao S, Chen H-L, Lo C-J, McLarty J (1996) Motif identification neural design for rapid and sensitive protein family search. CABIOS 12: 109-118
    • (1996) CABIOS , vol.12 , pp. 109-118
    • Wu, C.H.1    Zhao, S.2    Chen, H.-L.3    Lo, C.-J.4    McLarty, J.5
  • 150
    • 0242330716 scopus 로고    scopus 로고
    • Assessment of RAPTOR'S linear programming approach in CAFASP3
    • Xu J, Li M (2003) Assessment of RAPTOR'S linear programming approach in CAFASP3. Proteins: Structure, Function, and Genetics, 53(6):579-584
    • (2003) Proteins: Structure, Function, and Genetics , vol.53 , Issue.6 , pp. 579-584
    • Xu, J.1    Li, M.2
  • 152
    • 14844347376 scopus 로고    scopus 로고
    • Protein threading by linear programming: Theoretical analysis and computational results
    • Xu J, Li M, Xu Y (2004) Protein threading by linear programming: Theoretical analysis and computational results. J. of Combinatorial Optimization, 8(4):403-418
    • (2004) J. of Combinatorial Optimization , vol.8 , Issue.4 , pp. 403-418
    • Xu, J.1    Li, M.2    Xu, Y.3
  • 153
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • Yona G, Levitt M (2002) Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. Journal of Molecular Biology 315: 1257-1275
    • (2002) Journal of Molecular Biology , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 155
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein folds
    • Zhang Y, Skolnick J (2004) SPICKER: A clustering approach to identify near-native protein folds. J. Comput. Chem 25: 865-71
    • (2004) J. Comput. Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.