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Volumn 42, Issue W1, 2014, Pages

PredictProtein - An open resource for online prediction of protein structural and functional features

(20)  Yachdav, Guy a,b   Kloppmann, Edda a,c   Kajan, Laszlo a   Hecht, Maximilian a   Goldberg, Tatyana a   Hamp, Tobias a   Hönigschmid, Peter a   Schafferhans, Andrea a   Roos, Manfred a   Bernhofer, Michael a   Richter, Lothar a   Ashkenazy, Haim d   Punta, Marco a,e   Schlessinger, Avner f   Bromberg, Yana b,g   Schneider, Reinhard h   Vriend, Gerrit i   Sander, Chris j   Ben Tal, Nir k   Rost, Burkhard a,b,c,d  


Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION SERVICE PROVIDER; ARTICLE; CLIENT SERVER APPLICATION; COMPUTER INTERFACE; COMPUTER PROGRAM; INFORMATION RETRIEVAL; INFORMATION SERVICE; INTERNET; MEDICAL INFORMATICS; MEDICAL INFORMATION SYSTEM; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; SYSTEM ANALYSIS;

EID: 84904418029     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku366     Document Type: Article
Times cited : (504)

References (63)
  • 1
    • 79960976768 scopus 로고    scopus 로고
    • UniProt Knowledgebase: A hub of integrated protein data
    • Magrane,M. and Consortium,U. (2011) UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford), 2011, bar009.
    • (2011) Database (Oxford) , vol.2011
    • Magrane, M.1    Consortium, U.2
  • 2
    • 65449143636 scopus 로고    scopus 로고
    • New in protein structure and function annotation: Hotspots, single nucleotide polymorphisms and the 'Deep Web'
    • Bromberg,Y., Yachdav,G., Ofran,Y., Schneider,R. and Rost,B. (2009) New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'. Curr. Opin. Drug Discov. Devel., 12, 408-419.
    • (2009) Curr. Opin. Drug Discov. Devel. , vol.12 , pp. 408-419
    • Bromberg, Y.1    Yachdav, G.2    Ofran, Y.3    Schneider, R.4    Rost, B.5
  • 4
    • 74249119329 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction-Round VIII
    • Moult,J., Fidelis,K., Kryshtafovych,A., Rost,B. and Tramontano,A. (2009) Critical assessment of methods of protein structure prediction-Round VIII. Proteins, 77, 1-4.
    • (2009) Proteins , vol.77 , pp. 1-4
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Rost, B.4    Tramontano, A.5
  • 5
    • 0028783819 scopus 로고
    • Progress of 1D protein structure prediction at last
    • Rost,B. and Sander,C. (1995) Progress of 1D protein structure prediction at last. Proteins: Struct. Funct. Genet., 23, 295-300.
    • (1995) Proteins: Struct. Funct. Genet. , vol.23 , pp. 295-300
    • Rost, B.1    Sander, C.2
  • 6
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost,B. and Sander,C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
    • (1993) J. Mol. Biol. , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 9
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 10
    • 0036467068 scopus 로고    scopus 로고
    • Alignments grow, secondary structure prediction improves
    • Przybylski,D. and 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
  • 15
    • 0029889988 scopus 로고    scopus 로고
    • PHD: Predicting one-dimensional protein structure by profile-based neural networks
    • Rost,B. (1996) PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol., 266, 525-539.
    • (1996) Methods Enzymol. , vol.266 , pp. 525-539
    • Rost, B.1
  • 16
    • 0035782925 scopus 로고    scopus 로고
    • Review: Protein secondary structure prediction continues to rise
    • Rost,B. (2001) Review: protein secondary structure prediction continues to rise. J. Struct. Biol., 134, 204-218.
    • (2001) J. Struct. Biol. , vol.134 , pp. 204-218
    • Rost, B.1
  • 17
    • 33747846585 scopus 로고    scopus 로고
    • PROFtmb: A web server for predicting bacterial transmembrane beta barrel proteins
    • Bigelow,H. and Rost,B. (2006) PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res., 34, W186-W188.
    • (2006) Nucleic Acids Res. , vol.34
    • Bigelow, H.1    Rost, B.2
  • 18
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas,A., Van Dyke,M. and Stock,J. (1991) Predicting coiled coils from protein sequences. Science, 252, 1162-1164.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 19
    • 33747866099 scopus 로고    scopus 로고
    • DISULFIND: A disulfide bonding state and cysteine connectivity prediction server
    • Ceroni,A., Passerini,A., Vullo,A. and Frasconi,P. (2006) DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. Nucleic Acids Res., 34, W177-W181.
    • (2006) Nucleic Acids Res. , vol.34
    • Ceroni, A.1    Passerini, A.2    Vullo, A.3    Frasconi, P.4
  • 20
    • 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
  • 21
    • 34548750953 scopus 로고    scopus 로고
    • Natively unstructured regions in proteins identified from contact predictions
    • Schlessinger,A., Punta,M. and Rost,B. (2007) Natively unstructured regions in proteins identified from contact predictions. Bioinformatics, 23, 2376-2384.
    • (2007) Bioinformatics , vol.23 , pp. 2376-2384
    • Schlessinger, A.1    Punta, M.2    Rost, B.3
  • 22
    • 34547599318 scopus 로고    scopus 로고
    • Natively unstructured loops differ from other loops
    • Schlessinger,A., Liu,J. and Rost,B. (2007) Natively unstructured loops differ from other loops. PLoS Comput. Biol., 3, e140.
    • (2007) PLoS Comput. Biol. , vol.3
    • Schlessinger, A.1    Liu, J.2    Rost, B.3
  • 23
    • 24344503079 scopus 로고    scopus 로고
    • Protein flexibility and rigidity predicted from sequence
    • Schlessinger,A. and Rost,B. (2005) Protein flexibility and rigidity predicted from sequence. Proteins, 61, 115-126.
    • (2005) Proteins , vol.61 , pp. 115-126
    • Schlessinger, A.1    Rost, B.2
  • 24
    • 33645288849 scopus 로고    scopus 로고
    • PROFbval: Predict flexible and rigid residues in proteins
    • Schlessinger,A., Yachdav,G. and Rost,B. (2006) PROFbval: predict flexible and rigid residues in proteins. Bioinformatics, 22, 891-893.
    • (2006) Bioinformatics , vol.22 , pp. 891-893
    • Schlessinger, A.1    Yachdav, G.2    Rost, B.3
  • 25
    • 84885949386 scopus 로고    scopus 로고
    • Improved disorder prediction by combination of orthogonal approaches
    • Schlessinger,A., Punta,M., Yachdav,G., Kajan,L. and Rost,B. (2009) Improved disorder prediction by combination of orthogonal approaches. PLoS One, 4, e4433.
    • (2009) PLoS One , vol.4
    • Schlessinger, A.1    Punta, M.2    Yachdav, G.3    Kajan, L.4    Rost, B.5
  • 26
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    • Ashkenazy,H., Erez,E., Martz,E., Pupko,T. and Ben-Tal,N. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 38, W529-W533.
    • (2010) Nucleic Acids Res. , vol.38
    • Ashkenazy, H.1    Erez, E.2    Martz, E.3    Pupko, T.4    Ben-Tal, N.5
  • 28
    • 85047688149 scopus 로고    scopus 로고
    • News from the protein mutability landscape
    • Hecht,M., Bromberg,Y. and Rost,B. (2013) News from the protein mutability landscape. J. Mol. Biol., 425, 3937-3948.
    • (2013) J. Mol. Biol. , vol.425 , pp. 3937-3948
    • Hecht, M.1    Bromberg, Y.2    Rost, B.3
  • 32
    • 13444280419 scopus 로고    scopus 로고
    • PDB TM: Selection and membrane localization of transmembrane proteins in the protein data bank
    • Tusnady,G.E., Dosztanyi,Z. and Simon,I. (2005) PDB TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res., 33, D275-D278.
    • (2005) Nucleic Acids Res. , vol.33
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 34
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: Discriminating signal peptides from transmembrane regions
    • Petersen,T.N., Brunak,S., von Heijne,G. and Nielsen,H. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods, 8, 785-786.
    • (2011) Nat. Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 35
    • 29144483361 scopus 로고    scopus 로고
    • An HMM posterior decoder for sequence feature prediction that includes homology information
    • Kall,L., Krogh,A. and Sonnhammer,E.L. (2005) An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics, 21(Suppl. 1), i251-i257.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.L.3
  • 36
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • Jones,D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics, 23, 538-544.
    • (2007) Bioinformatics , vol.23 , pp. 538-544
    • Jones, D.T.1
  • 38
    • 34547100092 scopus 로고    scopus 로고
    • SNAP: Predict effect of non-synonymous polymorphisms on function
    • Bromberg,Y. and Rost,B. (2007) SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res., 35, 3823-3835.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3823-3835
    • Bromberg, Y.1    Rost, B.2
  • 39
    • 70349334681 scopus 로고    scopus 로고
    • In silico mutagenesis: A case study of the melanocortin 4 receptor
    • Bromberg,Y., Overton,J., Vaisse,C., Leibel,R.L. and Rost,B. (2009) In silico mutagenesis: a case study of the melanocortin 4 receptor. Faseb J., 23, 3059-3069.
    • (2009) Faseb J. , vol.23 , pp. 3059-3069
    • Bromberg, Y.1    Overton, J.2    Vaisse, C.3    Leibel, R.L.4    Rost, B.5
  • 40
    • 84908159485 scopus 로고    scopus 로고
    • HeatMapViewer:interactive display of 2D data in biology
    • doi:10.12688/f1000research.3-48.v1
    • Yachdav,G., Hecht,M., Yeheskel,A., Pasmanik-Chor,M. and Rost,B. (2014) HeatMapViewer:interactive display of 2D data in biology. F1000Research, 3, doi:10.12688/f1000research.3-48.v1.
    • (2014) F1000Research , pp. 3
    • Yachdav, G.1    Hecht, M.2    Yeheskel, A.3    Pasmanik-Chor, M.4    Rost, B.5
  • 41
    • 84866461910 scopus 로고    scopus 로고
    • LocTree2 predicts localization for all domains of life
    • Goldberg,T., Hamp,T. and Rost,B. (2012) LocTree2 predicts localization for all domains of life. Bioinformatics, 28, i458-i465.
    • (2012) Bioinformatics , vol.28
    • Goldberg, T.1    Hamp, T.2    Rost, B.3
  • 44
    • 84878095702 scopus 로고    scopus 로고
    • FFPred 2.0: Improved homology-independent prediction of gene ontology terms for eukaryotic protein sequences
    • Minneci,F., Piovesan,D., Cozzetto,D. and Jones,D.T. (2013) FFPred 2.0: improved homology-independent prediction of gene ontology terms for eukaryotic protein sequences. PLoS One, 8, e63754.
    • (2013) PLoS One , vol.8
    • Minneci, F.1    Piovesan, D.2    Cozzetto, D.3    Jones, D.T.4
  • 45
    • 21444454088 scopus 로고    scopus 로고
    • PROFcon: Novel prediction of long-range contacts
    • Punta,M. and Rost,B. (2005) PROFcon: novel prediction of long-range contacts. Bioinformatics, 21, 2960-2968.
    • (2005) Bioinformatics , vol.21 , pp. 2960-2968
    • Punta, M.1    Rost, B.2
  • 46
    • 0036968309 scopus 로고    scopus 로고
    • Loopy proteins appear conserved in evolution
    • Liu,J., Tan,H. and Rost,B. (2002) Loopy proteins appear conserved in evolution. J. Mol. Biol., 322, 53-64.
    • (2002) J. Mol. Biol. , vol.322 , pp. 53-64
    • Liu, J.1    Tan, H.2    Rost, B.3
  • 47
    • 0041620131 scopus 로고    scopus 로고
    • NORSp: Predictions of long regions without regular secondary structure
    • Liu,J. and Rost,B. (2003) NORSp: predictions of long regions without regular secondary structure. Nucleic Acids Res., 31, 3833-3835.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3833-3835
    • Liu, J.1    Rost, B.2
  • 48
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • Dosztanyi,Z., Csizmok,V., Tompa,P. and Simon,I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 50
    • 77956502766 scopus 로고    scopus 로고
    • Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources
    • Mizianty,M.J., Stach,W., Chen,K., Kedarisetti,K.D., Disfani,F.M. and Kurgan,L. (2010) Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Bioinformatics, 26, i489-i496.
    • (2010) Bioinformatics , vol.26
    • Mizianty, M.J.1    Stach, W.2    Chen, K.3    Kedarisetti, K.D.4    Disfani, F.M.5    Kurgan, L.6
  • 52
    • 33846662784 scopus 로고    scopus 로고
    • ISIS: Interaction sites identified from sequence
    • Ofran,Y. and Rost,B. (2007) ISIS: interaction sites identified from sequence. Bioinformatics, 23, e13-e16.
    • (2007) Bioinformatics , vol.23
    • Ofran, Y.1    Rost, B.2
  • 53
    • 84866063123 scopus 로고    scopus 로고
    • Alternative protein-protein interfaces are frequent exceptions
    • Hamp,T. and Rost,B. (2012) Alternative protein-protein interfaces are frequent exceptions. PLoS Comput. Biol., 8, e1002623.
    • (2012) PLoS Comput. Biol. , vol.8
    • Hamp, T.1    Rost, B.2
  • 54
    • 84904820098 scopus 로고    scopus 로고
    • Technische Universität München,Munich, Germany
    • Hönigschmid,P. (2012) Diploma thesis, Technische Universität München,Munich, Germany.
    • (2012) Diploma Thesis
    • Hönigschmid, P.1
  • 56
    • 4143051195 scopus 로고    scopus 로고
    • Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior
    • Mayrose,I., Graur,D., Ben-Tal,N. and Pupko,T. (2004) Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol. Biol. Evol., 21, 1781-1791.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1781-1791
    • Mayrose, I.1    Graur, D.2    Ben-Tal, N.3    Pupko, T.4
  • 57
    • 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,R.E., Mayrose,I., Glaser,F. and Ben-Tal,N. (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, 18(Suppl. 1), S71-S77.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 62
    • 46949102023 scopus 로고    scopus 로고
    • Transmembrane protein 85 from both human (TMEM85) and yeast (YGL231c) inhibit hydrogen peroxide mediated cell death in yeast
    • Ring,G., Khoury,C.M., Solar,A.J., Yang,Z., Mandato,C.A. and Greenwood,M.T. (2008) Transmembrane protein 85 from both human (TMEM85) and yeast (YGL231c) inhibit hydrogen peroxide mediated cell death in yeast. FEBS Lett., 582, 2637-2642.
    • (2008) FEBS Lett. , vol.582 , pp. 2637-2642
    • Ring, G.1    Khoury, C.M.2    Solar, A.J.3    Yang, Z.4    Mandato, C.A.5    Greenwood, M.T.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.