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Volumn 33, Issue SUPPL. 2, 2005, Pages

FFAS03: A server for profile-profile sequence alignments

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 23144463912     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki418     Document Type: Article
Times cited : (427)

References (32)
  • 1
    • 0027057526 scopus 로고
    • A database of protein structure families with common folding motifs
    • Holm,L., Ouzounis,C., Sander,C., Tuparev,G. and Vriend,G. (1992) A database of protein structure families with common folding motifs. Protein Sci., 1, 1691-1698.
    • (1992) Protein Sci. , vol.1 , pp. 1691-1698
    • Holm, L.1    Ouzounis, C.2    Sander, C.3    Tuparev, G.4    Vriend, G.5
  • 3
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski,L., Jaroszewski,L., Li,W. and 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
  • 4
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3836-3845
    • Pietrokovski, S.1
  • 5
    • 0033846832 scopus 로고    scopus 로고
    • Improving the quality of twilight-zone alignments
    • Jaroszewski,L., Rychlewski,L. and Godzik,A. (2000) Improving the quality of twilight-zone alignments. Protein Sci., 9, 1487-1496.
    • (2000) Protein Sci. , vol.9 , pp. 1487-1496
    • Jaroszewski, L.1    Rychlewski, L.2    Godzik, A.3
  • 6
    • 0242267517 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP )-round V
    • Moult,J., Fidelis,K., Zemla,A. and Hubbard,T. (2003) Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins, 53(Suppl. 6), 334-339.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 334-339
    • Moult, J.1    Fidelis, K.2    Zemla, A.3    Hubbard, T.4
  • 8
    • 0035103763 scopus 로고    scopus 로고
    • LiveBench-1: Continuous benchmarking of protein structure prediction servers
    • Bujnicki,J.M., Elofsson,A., Fischer,D. and Rychlewski,L. (2001) LiveBench-1: Continuous benchmarking of protein structure prediction servers. Protein Sci., 10, 352-361.
    • (2001) Protein Sci. , vol.10 , pp. 352-361
    • Bujnicki, J.M.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 9
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • Yona,G. and Levitt,M. (2002) Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.
    • (2002) J. Mol. Biol. , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 10
    • 0141634362 scopus 로고    scopus 로고
    • Profile-profile comparisons by COMPASS predict intricate homologies between protein families
    • Sadreyev,R.I., Baker,D. and Grishin,N.V. (2003) Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci., 12, 2262-2272.
    • (2003) Protein Sci. , vol.12 , pp. 2262-2272
    • Sadreyev, R.I.1    Baker, D.2    Grishin, N.V.3
  • 11
    • 4444298729 scopus 로고    scopus 로고
    • Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods
    • Ohlson,T., Wallner,B. and Elofsson,A. (2004) Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods. Proteins, 57, 188-197.
    • (2004) Proteins , vol.57 , pp. 188-197
    • Ohlson, T.1    Wallner, B.2    Elofsson, A.3
  • 12
    • 1842559320 scopus 로고    scopus 로고
    • Alignment of protein sequences by their profiles
    • Marti-Renom,M.A., Madhusudhan,M.S. and Sali,A. (2004) Alignment of protein sequences by their profiles. Protein Sci., 13, 1071-1087.
    • (2004) Protein Sci. , vol.13 , pp. 1071-1087
    • Marti-Renom, M.A.1    Madhusudhan, M.S.2    Sali, A.3
  • 13
    • 2442663920 scopus 로고    scopus 로고
    • Scoring profile-to-profile sequence alignments
    • Wang,G. and Dunbrack,R.L.,Jr (2004) Scoring profile-to-profile sequence alignments. Protein Sci., 13, 1612-1626.
    • (2004) Protein Sci. , vol.13 , pp. 1612-1626
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 14
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 15
    • 0035072551 scopus 로고    scopus 로고
    • Clustering of highly homologous sequences to reduce the size of large protein databases
    • Li,W., Jaroszewski,L. and Godzik,A. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics, 17, 282-283.
    • (2001) Bioinformatics , vol.17 , pp. 282-283
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 16
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
    • (1996) Methods Enzymol. , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 19
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: A tool for genome-scale analysis of protein functions and evolution
    • Tatusov,R.L., Galperin,M.Y., Natale,DA. and Koonin,E.V. (2000) The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res., 28, 33-36.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 22
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 23
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu,A.A., Shelenkov,A.A. and Dunbrack,R.L.,Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci., 12, 2001-2014.
    • (2003) Protein Sci. , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 24
    • 0036893072 scopus 로고    scopus 로고
    • Rapid protein domain assignment from amino acid sequence using predicted secondary structure
    • Marsden,R.L., McGuffin,L.J. and Jones,D.T. (2002) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci., 11, 2814-2824.
    • (2002) Protein Sci. , vol.11 , pp. 2814-2824
    • Marsden, R.L.1    McGuffin, L.J.2    Jones, D.T.3
  • 25
    • 0042622240 scopus 로고    scopus 로고
    • GlobPlot: Exploring protein sequences for globularity and disorder
    • Linding,R., Russell,R.B., Neduva,V. and Gibson,T.J. (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res., 31, 3701-3708.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3701-3708
    • Linding, R.1    Russell, R.B.2    Neduva, V.3    Gibson, T.J.4
  • 26
    • 33645124756 scopus 로고    scopus 로고
    • Structure and mechanism of the apoptotic protease activating factor 1 (Apaf-1)
    • in press
    • Riedl,S.J., Li,W., Chao,Y., Schwarzenbacher,R. and Shi,Y. (2005) Structure and mechanism of the apoptotic protease activating factor 1 (Apaf-1). Nature, in press.
    • (2005) Nature
    • Riedl, S.J.1    Li, W.2    Chao, Y.3    Schwarzenbacher, R.4    Shi, Y.5
  • 27
    • 0034658130 scopus 로고    scopus 로고
    • ATP-activated oligomerization as a mechanism for apoptosis regulation: Fold and mechanism prediction for CED-4
    • Jaroszewski,L., Rychlewski,L., Reed,J.C. and Godzik,A. (2000) ATP-activated oligomerization as a mechanism for apoptosis regulation: fold and mechanism prediction for CED-4. Proteins, 39, 197-203.
    • (2000) Proteins , vol.39 , pp. 197-203
    • Jaroszewski, L.1    Rychlewski, L.2    Reed, J.C.3    Godzik, A.4
  • 28
    • 2942610866 scopus 로고    scopus 로고
    • Domain analysis of the tubulin cofactor system: A model for tubulin folding and dimerization
    • Grynberg,M., Jaroszewski,L. and Godzik,A. (2003) Domain analysis of the tubulin cofactor system: A model for tubulin folding and dimerization. BMC Bioinformatics, 4, 46.
    • (2003) BMC Bioinformatics , vol.4 , pp. 46
    • Grynberg, M.1    Jaroszewski, L.2    Godzik, A.3
  • 31
    • 3242887695 scopus 로고    scopus 로고
    • Protein structure prediction and analysis using the Roberta server
    • Kim,D.E., Chivian,D. and Baker,D. (2004) Protein structure prediction and analysis using the Roberta server. Nucleic Acids Res., 32, W526-W531.
    • (2004) Nucleic Acids Res. , vol.32
    • Kim, D.E.1    Chivian, D.2    Baker, D.3
  • 32
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • Ginalski,K., Elofsson,A., Fischer,D. and Rychlewski,L. (2003) 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.