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Volumn 62, Issue 2, 2006, Pages 343-355

Will my protein crystallize? A sequence-based predictor

Author keywords

Machine learning; Protein crystallization; Protein structure determination; Sequence comparison; Structural genomics

Indexed keywords

AMINO ACID; DIPEPTIDE; PEPTIDE; TRIPEPTIDE;

EID: 30144445696     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20789     Document Type: Article
Times cited : (72)

References (56)
  • 1
    • 0033757822 scopus 로고    scopus 로고
    • An overview of structural genomics
    • Burley SK. An overview of structural genomics. Nat Struct Biol 2000;7(Suppl):932-934.
    • (2000) Nat Struct Biol , vol.7 , pp. 932-934
    • Burley, S.K.1
  • 4
    • 0037349452 scopus 로고    scopus 로고
    • Structural proteomics: Toward high-throughput structural biology as a tool in functional genomics
    • Yee A, Pardee K, Christendat D, Savchenko A, Edwards AM, Arrowsmith CH. Structural proteomics: toward high-throughput structural biology as a tool in functional genomics. Acc Chem Res 2003;36:183-189.
    • (2003) Acc Chem Res , vol.36 , pp. 183-189
    • Yee, A.1    Pardee, K.2    Christendat, D.3    Savchenko, A.4    Edwards, A.M.5    Arrowsmith, C.H.6
  • 8
    • 0348014440 scopus 로고    scopus 로고
    • TEXTAL system: Artificial intelligence techniques for automated protein model building
    • Ioerger TR, Sacchettini JC. TEXTAL system: artificial intelligence techniques for automated protein model building. Methods Enzymol 2003;374:244-270.
    • (2003) Methods Enzymol , vol.374 , pp. 244-270
    • Ioerger, T.R.1    Sacchettini, J.C.2
  • 10
    • 0037202215 scopus 로고    scopus 로고
    • Longitudinal (1)H relaxation optimization in TROSY NMR spectroscopy
    • Pervushin K, Vogeli B, Eletsky A. Longitudinal (1)H relaxation optimization in TROSY NMR spectroscopy. J Am Chem Soc 2002;124:12898-12902.
    • (2002) J Am Chem Soc , vol.124 , pp. 12898-12902
    • Pervushin, K.1    Vogeli, B.2    Eletsky, A.3
  • 11
    • 0037120882 scopus 로고    scopus 로고
    • Solution NMR techniques for large molecular and supramolecular structures
    • Riek R, Fiaux J, Bertelsen EB, Horwich AL, Wuthrich K. Solution NMR techniques for large molecular and supramolecular structures. J Am Chem Soc 2002;124:12144-12153.
    • (2002) J Am Chem Soc , vol.124 , pp. 12144-12153
    • Riek, R.1    Fiaux, J.2    Bertelsen, E.B.3    Horwich, A.L.4    Wuthrich, K.5
  • 12
    • 0036361601 scopus 로고    scopus 로고
    • Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools
    • Monleon D, Colson K, Moseley HN, Anklin C, Oswald R, Szyperski T, Montelione GT. Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools. J Struct Funct Genomics 2002;2:93-101.
    • (2002) J Struct Funct Genomics , vol.2 , pp. 93-101
    • Monleon, D.1    Colson, K.2    Moseley, H.N.3    Anklin, C.4    Oswald, R.5    Szyperski, T.6    Montelione, G.T.7
  • 15
    • 8844222708 scopus 로고    scopus 로고
    • TargetDB: A target registration database for structural genomics projects
    • Chen L, Oughtred R, Berman HM, Westbrook J. TargetDB: a target registration database for structural genomics projects. Bioinformatics 2004;20:2860-2862.
    • (2004) Bioinformatics , vol.20 , pp. 2860-2862
    • Chen, L.1    Oughtred, R.2    Berman, H.M.3    Westbrook, J.4
  • 17
    • 0038580657 scopus 로고    scopus 로고
    • Strategies and methods in the identification of antagonists of protein-protein interactions
    • Gadek TR. Strategies and methods in the identification of antagonists of protein-protein interactions. Biotechniques 2003;Suppl: 21-24.
    • (2003) Biotechniques , Issue.SUPPL. , pp. 21-24
    • Gadek, T.R.1
  • 20
    • 8544275816 scopus 로고    scopus 로고
    • Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: Maximum clustering strategy for structural genomics
    • Canaves JM, Page R, Wilson IA, Stevens RC. Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J Mol Biol 2004;344:977-991.
    • (2004) J Mol Biol , vol.344 , pp. 977-991
    • Canaves, J.M.1    Page, R.2    Wilson, I.A.3    Stevens, R.C.4
  • 23
    • 0036975283 scopus 로고    scopus 로고
    • Datamining protein structure databanks for crystallization patterns of proteins
    • Valafar H, Prestegard JH, Valafar F. Datamining protein structure databanks for crystallization patterns of proteins. Ann N Y Acad Sci 2002;980:13-22.
    • (2002) Ann N Y Acad Sci , vol.980 , pp. 13-22
    • Valafar, H.1    Prestegard, J.H.2    Valafar, F.3
  • 26
    • 0031381525 scopus 로고    scopus 로고
    • Wrappers for feature subset selection
    • Kohavi R, John G. Wrappers for feature subset selection. Artif Intell J 1997;97:273-324.
    • (1997) Artif Intell J , vol.97 , pp. 273-324
    • Kohavi, R.1    John, G.2
  • 28
    • 0035072551 scopus 로고    scopus 로고
    • Clustering of highly homologous sequences to reduce the size of large protein databases
    • Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 2001;17:282-283.
    • (2001) Bioinformatics , vol.17 , pp. 282-283
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 29
    • 0036169928 scopus 로고    scopus 로고
    • Tolerating some redundancy significantly speeds up clustering of large protein databases
    • Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 2002;18:77-82.
    • (2002) Bioinformatics , vol.18 , pp. 77-82
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 30
    • 0035233646 scopus 로고    scopus 로고
    • Optimality of the genetic code with respect to protein stability and amino-acid frequencies
    • RESEARCH0049
    • Gilis D, Massar S, Cerf NJ, Rooman M. Optimality of the genetic code with respect to protein stability and amino-acid frequencies. Genome Biol 2001;2:RESEARCH0049.
    • (2001) Genome Biol , vol.2
    • Gilis, D.1    Massar, S.2    Cerf, N.J.3    Rooman, M.4
  • 31
    • 0002629270 scopus 로고
    • Maximum likehood from incomplete data via the EM algorithm
    • Dempster AP, Laird NM, Rubin DB. Maximum likehood from incomplete data via the EM algorithm. J Roy Statist Soc 1977;39: 1-38.
    • (1977) J Roy Statist Soc , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3
  • 32
    • 0034826101 scopus 로고    scopus 로고
    • An experimental comparison of model-based clustering methods
    • Meila M, Heckerman D. An experimental comparison of model-based clustering methods. Machine Learning 2001;42:9-29.
    • (2001) Machine Learning , vol.42 , pp. 9-29
    • Meila, M.1    Heckerman, D.2
  • 33
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman DM, Steitz TA, Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem 1986;15:321-353.
    • (1986) Annu Rev Biophys Biophys Chem , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 34
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 36
    • 30144436644 scopus 로고    scopus 로고
    • Personal communication
    • Gilis D. Personal communication. 2004.
    • (2004)
    • Gilis, D.1
  • 42
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 43
    • 0026466041 scopus 로고
    • Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference
    • Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992;35:367-375.
    • (1992) J Mol Evol , vol.35 , pp. 367-375
    • Rzhetsky, A.1    Nei, M.2
  • 46
    • 0002419948 scopus 로고    scopus 로고
    • Beyond independence: Conditions for the optimality of the simple bayesian classifier
    • Saitta L, editor. San Francisco, CA: Morgan Kaufmann
    • Domingos P, Pazzani M. Beyond independence: conditions for the optimality of the simple bayesian classifier. In: Saitta L, editor. Machine Learning: Proceedings of the Thirteenth International Conference. San Francisco, CA: Morgan Kaufmann; 1996. p 105-112.
    • (1996) Machine Learning: Proceedings of the Thirteenth International Conference , pp. 105-112
    • Domingos, P.1    Pazzani, M.2
  • 47
    • 0003120218 scopus 로고    scopus 로고
    • Fast training of support vector machines using sequential minimal optimization
    • Scholkopf B, Surges CJC, Smola AJ, editors. Cambridge, MA: MIT Press
    • Platt J. Fast training of support vector machines using sequential minimal optimization. Scholkopf B, Surges CJC, Smola AJ, editors. Advances in kernal methods: support vector learning. Cambridge, MA: MIT Press; 1999. p 182-208.
    • (1999) Advances in Kernal Methods: Support Vector Learning , pp. 182-208
    • Platt, J.1
  • 50
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 54
    • 30144436970 scopus 로고    scopus 로고
    • Cost-sensitive classification using decision trees, boosting and MetaCost
    • Sarker R, Abbass H, Newton C, editors. Hershey, PA: Idea Group Publishing
    • Ting K. Cost-sensitive classification using decision trees, boosting and MetaCost. In Sarker R, Abbass H, Newton C, editors. Heuristic and optimization for knowledge discovery. Hershey, PA: Idea Group Publishing; 2002.
    • (2002) Heuristic and Optimization for Knowledge Discovery
    • Ting, K.1
  • 55
    • 30144439931 scopus 로고    scopus 로고
    • A study on the effest of class distribution using cost-sensitive learning
    • Ting K. A study on the effest of class distribution using cost-sensitive learning. Discovery Sci 2002:98-112.
    • (2002) Discovery Sci , pp. 98-112
    • Ting, K.1
  • 56
    • 30144439646 scopus 로고    scopus 로고
    • Personal communication
    • Majumdar S. Personal communication. 2005.
    • (2005)
    • Majumdar, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.