메뉴 건너뛰기




Volumn 56, Issue 3, 2004, Pages 528-538

DPANN: Improved sequence to structure alignments following fold recognition

Author keywords

Artificial neural networks; Distant homology modeling; Substitution matrix

Indexed keywords

PROTEIN;

EID: 3142771861     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20144     Document Type: Article
Times cited : (8)

References (50)
  • 3
    • 0034990892 scopus 로고    scopus 로고
    • Sequence- and structure-based protein function prediction from genomic information
    • Baxter SM, Fetrow JS. Sequence- and structure-based protein function prediction from genomic information. Curr Opin Drug Discov Devel 2001;4:291-295.
    • (2001) Curr Opin Drug Discov Devel , vol.4 , pp. 291-295
    • Baxter, S.M.1    Fetrow, J.S.2
  • 4
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • Casari G, Sander C, Valencia A. A method to predict functional residues in proteins. Nature Struct Biol 1995;2:171-178.
    • (1995) Nature Struct Biol , vol.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 7
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • Rost B. Enzyme function less conserved than anticipated. J Mol Biol 2002;318:595-608.
    • (2002) J Mol Biol , vol.318 , pp. 595-608
    • Rost, B.1
  • 8
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996;257:342-358.
    • (1996) J Mol Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 9
    • 0032483312 scopus 로고    scopus 로고
    • Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases
    • Fetrow JS, Skolnick J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J Mol Biol 1998;281:949-968.
    • (1998) J Mol Biol , vol.281 , pp. 949-968
    • Fetrow, J.S.1    Skolnick, J.2
  • 10
    • 0032932490 scopus 로고    scopus 로고
    • From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions
    • Zhang B, Rychlewski L, Pawlowski K, Fetrow JS, Skolnick J, Godzik A. From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions. Protein Sci 1999;8:1104-1115.
    • (1999) Protein Sci , vol.8 , pp. 1104-1115
    • Zhang, B.1    Rychlewski, L.2    Pawlowski, K.3    Fetrow, J.S.4    Skolnick, J.5    Godzik, A.6
  • 11
    • 0035059281 scopus 로고    scopus 로고
    • Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?
    • Fetrow JS, Siew N, Di Gennaro JA, Martinez-Yamout M, Dyson HJ, Skolnick J. Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight? Protein Sci 2001;10:1005-1014.
    • (2001) Protein Sci , vol.10 , pp. 1005-1014
    • Fetrow, J.S.1    Siew, N.2    Di Gennaro, J.A.3    Martinez-Yamout, M.4    Dyson, H.J.5    Skolnick, J.6
  • 13
    • 0035853280 scopus 로고    scopus 로고
    • Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
    • Landgraf R, Xenarios I, Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol 2001;307:1487-1502.
    • (2001) J Mol Biol , vol.307 , pp. 1487-1502
    • Landgraf, R.1    Xenarios, I.2    Eisenberg, D.3
  • 14
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    • Armon A, Graur D, Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 2001;307:447-463.
    • (2001) J Mol Biol , vol.307 , pp. 447-463
    • Armon, A.1    Graur, D.2    Ben-Tal, N.3
  • 15
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 2002;18(Suppl 1):S71-7.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 18
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 20
    • 0037228878 scopus 로고    scopus 로고
    • Twenty thousand ORFan microbial protein families for the biologist?
    • Siew N, Fischer D. Twenty thousand ORFan microbial protein families for the biologist? Structure (Camb) 2003;11:7-9.
    • (2003) Structure (Camb) , vol.11 , pp. 7-9
    • Siew, N.1    Fischer, D.2
  • 21
    • 0034126813 scopus 로고    scopus 로고
    • Protein structure prediction in the postgenomic era
    • Jones DT. Protein structure prediction in the postgenomic era. Curr Opin Struct Biol 2000;10:371-379.
    • (2000) Curr Opin Struct Biol , vol.10 , pp. 371-379
    • Jones, D.T.1
  • 22
    • 0034060287 scopus 로고    scopus 로고
    • Structural genomics and its importance for gene function analysis
    • Skolnick J, Fetrow JS, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol 2000;18:283-287.
    • (2000) Nat Biotechnol , vol.18 , pp. 283-287
    • Skolnick, J.1    Fetrow, J.S.2    Kolinski, A.3
  • 23
    • 0032751746 scopus 로고    scopus 로고
    • Predicting protein three-dimensional structure
    • Moult J. Predicting protein three-dimensional structure. Curr Opin Biotechnol 1999;10:583-588.
    • (1999) Curr Opin Biotechnol , vol.10 , pp. 583-588
    • Moult, J.1
  • 24
    • 0031307020 scopus 로고    scopus 로고
    • Competitive assessment of protein fold recognition and alignment accuracy
    • Levitt M. Competitive assessment of protein fold recognition and alignment accuracy. Proteins 1997;Suppl 1:92-104.
    • (1997) Proteins , vol.1 , Issue.SUPPL. , pp. 92-104
    • Levitt, M.1
  • 25
    • 0031303337 scopus 로고    scopus 로고
    • A retrospective analysis of CASP2 threading predictions
    • Marchler-Bauer A, Levitt M, Bryant SH. A retrospective analysis of CASP2 threading predictions. Proteins 1997;Suppl 1:83-91.
    • (1997) Proteins , vol.1 , Issue.SUPPL. , pp. 83-91
    • Marchler-Bauer, A.1    Levitt, M.2    Bryant, S.H.3
  • 26
    • 0032619001 scopus 로고    scopus 로고
    • An attempt to analyse progress in fold recognition from CASP1 to CASP3
    • Sippl MJ, Lackner P, Domingues FS, Koppensteiner WA. An attempt to analyse progress in fold recognition from CASP1 to CASP3. Proteins 1999;Suppl 3:226-230.
    • (1999) Proteins , vol.3 , Issue.SUPPL. , pp. 226-230
    • Sippl, M.J.1    Lackner, P.2    Domingues, F.S.3    Koppensteiner, W.A.4
  • 29
    • 84972546031 scopus 로고
    • Sequence comparison significance and poisson approximation
    • Waterman MS, Vingron M. Sequence comparison significance and poisson approximation. Statistical Science 1994;9:367-381.
    • (1994) Statistical Science , vol.9 , pp. 367-381
    • Waterman, M.S.1    Vingron, M.2
  • 30
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 32
    • 0037083541 scopus 로고    scopus 로고
    • A study on protein sequence alignment quality
    • Elofsson A. A study on protein sequence alignment quality. Proteins 2002;46:330-339.
    • (2002) Proteins , vol.46 , pp. 330-339
    • Elofsson, A.1
  • 33
    • 0035937260 scopus 로고    scopus 로고
    • Pairwise sequence alignment below the twilight zone
    • Blake JD, Cohen FE. Pairwise sequence alignment below the twilight zone. J Mol Biol 2001;307:721-735.
    • (2001) J Mol Biol , vol.307 , pp. 721-735
    • Blake, J.D.1    Cohen, F.E.2
  • 34
    • 0036145804 scopus 로고    scopus 로고
    • A comparison of position-specific score matrices based on sequence and structure alignments
    • Panchenko AR, Bryant SH. A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci 2002;11:361-370.
    • (2002) Protein Sci , vol.11 , pp. 361-370
    • Panchenko, A.R.1    Bryant, S.H.2
  • 35
    • 0037103044 scopus 로고    scopus 로고
    • Comparison of sequence and structure alignments for protein domains
    • Marchler-Bauer A, Panchenko AR, Ariel N, Bryant SH. Comparison of sequence and structure alignments for protein domains. Proteins 2002;15:439-446.
    • (2002) Proteins , vol.15 , pp. 439-446
    • Marchler-Bauer, A.1    Panchenko, A.R.2    Ariel, N.3    Bryant, S.H.4
  • 36
    • 0036081436 scopus 로고    scopus 로고
    • In search for more accurate alignments in the twilight zone
    • Jaroszewski L, Li W, Godzik A. In search for more accurate alignments in the twilight zone. Protein Sci 2002;11:1702-1713.
    • (2002) Protein Sci , vol.11 , pp. 1702-1713
    • Jaroszewski, L.1    Li, W.2    Godzik, A.3
  • 37
    • 0035749546 scopus 로고    scopus 로고
    • Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement
    • Skolnick J, Kolinski A, Kihara D, Betancourt M, Rotkiewicz P, Boniecki M. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins 2001;Suppl 5:149-156.
    • (2001) Proteins , vol.5 , Issue.SUPPL. , pp. 149-156
    • Skolnick, J.1    Kolinski, A.2    Kihara, D.3    Betancourt, M.4    Rotkiewicz, P.5    Boniecki, M.6
  • 38
    • 0035427225 scopus 로고    scopus 로고
    • Generalized comparative modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement
    • Kolinski A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins 2001;44:133-149.
    • (2001) Proteins , vol.44 , pp. 133-149
    • Kolinski, A.1    Betancourt, M.R.2    Kihara, D.3    Rotkiewicz, P.4    Skolnick, J.5
  • 39
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • Lassmann T, Sonnhammer EL. Quality assessment of multiple alignment programs. FEBS Lett 2002;529:126-130.
    • (2002) FEBS Lett , vol.529 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 40
    • 0033846832 scopus 로고    scopus 로고
    • Improving the quality of twilight-zone alignments
    • Jaroszewski L, Rychlewski L, Godzik A. Improving the quality of twilight-zone alignments. Protein Sci 2000;9:1487-1496.
    • (2000) Protein Sci , vol.9 , pp. 1487-1496
    • Jaroszewski, L.1    Rychlewski, L.2    Godzik, A.3
  • 41
    • 0037058927 scopus 로고    scopus 로고
    • The directional atomic solvation energy: An atom-based potential for the assignment of protein sequences to known folds
    • Mallick P, Weiss R, Eisenberg D. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc Natl Acad Sci USA 2002;99:16041-16046.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 16041-16046
    • Mallick, P.1    Weiss, R.2    Eisenberg, D.3
  • 43
    • 0029889988 scopus 로고    scopus 로고
    • Phd - Predicting one-dimensional protein-structure by profile-based neural networks
    • Rost B. Phd - predicting one-dimensional protein-structure by profile-based neural networks. Methods Enzymol 1996;266:525-539.
    • (1996) Methods Enzymol , vol.266 , pp. 525-539
    • Rost, B.1
  • 44
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 46
    • 3142767837 scopus 로고    scopus 로고
    • Martin ACR. http://www.bioinf.org.uk/software/profit/.
    • Martin, A.C.R.1
  • 47
    • 0000009443 scopus 로고
    • Rapid comparison of protein structures
    • McLachlan AD. Rapid comparison of protein structures. Acta Crystallogr A 1982;38:871-873.
    • (1982) Acta Crystallogr A , vol.38 , pp. 871-873
    • McLachlan, A.D.1
  • 48
    • 0032606076 scopus 로고    scopus 로고
    • Some measures of comparative performance in the three CASPs
    • Venclovas C, Zemla A, Fidelis K, Moult J. Some measures of comparative performance in the three CASPs. Proteins 1999; Suppl 3:231-237.
    • (1999) Proteins , vol.3 , Issue.SUPPL. , pp. 231-237
    • Venclovas, C.1    Zemla, A.2    Fidelis, K.3    Moult, J.4
  • 49
    • 0030310317 scopus 로고    scopus 로고
    • Assessing the performance of fold recognition methods by means of a comprehensive benchmark
    • Fischer D, Elofsson A, Rice D, Eisenberg D. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pac Symp Biocomput 1996:300-318.
    • (1996) Pac Symp Biocomput , pp. 300-318
    • Fischer, D.1    Elofsson, A.2    Rice, D.3    Eisenberg, D.4
  • 50
    • 0141978673 scopus 로고    scopus 로고
    • Comparative protein structure modeling by iterative alignment, model building and model assessment
    • John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 2003;31:3982-3992.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3982-3992
    • John, B.1    Sali, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.