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Volumn 9783709109472, Issue , 2012, Pages 111-143

Protein sequence-structure-function-network links discovered with the ANNOTATOR software suite: Application to ELYS/Mel-28

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMS;

EID: 84930713754     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-0947-2_7     Document Type: Chapter
Times cited : (7)

References (146)
  • 1
    • 33646855259 scopus 로고    scopus 로고
    • Accelrys, San Diego. Accessed 02 Dec 2011
    • Accelrys (2011) Pipeline pilot. Accelrys, San Diego. http://accelrys.com/products/pipeline-pilot/. Accessed 02 Dec 2011
    • (2011) Pipeline Pilot
  • 2
    • 80052635233 scopus 로고    scopus 로고
    • Changes in tear protein profile in keratoconus disease
    • Acera A, Vecino E, Rodriguez-Agirretxe I et al (2011) Changes in tear protein profile in keratoconus disease. Eye 25:1225-1233
    • (2011) Eye , vol.25 , pp. 1225-1233
    • Acera, A.1    Vecino, E.2    Rodriguez-Agirretxe, I.3
  • 3
    • 36749045172 scopus 로고    scopus 로고
    • The molecular architecture of the nuclear pore complex
    • Alber F, Dokudovskaya S, Veenhoff LM et al (2007) The molecular architecture of the nuclear pore complex. Nature 450:695-701. doi:10.1038/nature06405
    • (2007) Nature , vol.450 , pp. 695-701
    • Alber, F.1    Dokudovskaya, S.2    Veenhoff, L.M.3
  • 4
  • 5
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403-410. doi:10.1016/S0022-2836(05)80360-2
    • (1990) J Mol Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3
  • 6
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 7
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: Application to microtubules and the ribosome
    • Baker NA, Sept D, Joseph S et al (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037-10041. doi:10.1073/pnas.181342398
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3
  • 8
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3. 0
    • Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783-795. doi:10.1016/j.jmb.2004.05.028
    • (2004) J Mol Biol , vol.340 , pp. 783-795
    • Bendtsen, J.D.1    Nielsen, H.2    Von Heijne, G.3    Brunak, S.4
  • 10
    • 62649147821 scopus 로고    scopus 로고
    • Sequence context-specific profiles for homology searching
    • Biegert A, Soding J (2009) Sequence context-specific profiles for homology searching. Proc Natl Acad Sci 106:3770-3775. doi:10.1073/pnas.0810767106
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 3770-3775
    • Biegert, A.1    Soding, J.2
  • 11
    • 0032491377 scopus 로고    scopus 로고
    • Predicting function: From genes to genomes and back
    • Bork P, Dandekar T, Diaz-Lazcoz Y et al (1998) Predicting function: from genes to genomes and back. J Mol Biol 283:707-725. doi:10.1006/jmbi.1998.2144
    • (1998) J Mol Biol , vol.283 , pp. 707-725
    • Bork, P.1    Dandekar, T.2    Diaz-Lazcoz, Y.3
  • 12
    • 0026520770 scopus 로고
    • Methods and algorithms for statistical analysis of protein sequences
    • Brendel V, Bucher P, Nourbakhsh IR et al (1992) Methods and algorithms for statistical analysis of protein sequences. Proc Natl Acad Sci USA 89:2002-2006
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2002-2006
    • Brendel, V.1    Bucher, P.2    Nourbakhsh, I.R.3
  • 13
    • 84930728451 scopus 로고    scopus 로고
    • CLC Bio, Aarhus. Accessed 02 Dec 2011
    • CLC Bio (2011) CLC genomics workbench. CLC Bio, Aarhus. http://www.clcbio.com/. Accessed 02 Dec 2011
    • (2011) CLC Genomics Workbench
  • 14
    • 0028568176 scopus 로고
    • TopPred II: An improved software for membrane protein structure predictions
    • Claros MG, von Heijne G (1994) TopPred II: an improved software for membrane protein structure predictions. Comput Appl Biosci 10:685-686
    • (1994) Comput Appl Biosci , vol.10 , pp. 685-686
    • Claros, M.G.1    Von Heijne, G.2
  • 15
    • 0001282761 scopus 로고
    • Information enhancement methods for large scale sequence analysis
    • Claverie J-M, States DJ (1993) Information enhancement methods for large scale sequence analysis. Comput Chem 17:191-201. doi:10.1016/0097-8485(93)85010-A
    • (1993) Comput Chem , vol.17 , pp. 191-201
    • Claverie, J.-M.1    States, D.J.2
  • 17
    • 48449106792 scopus 로고    scopus 로고
    • The Jpred 3 secondary structure prediction server
    • Cole C, Barber JD, Barton GJ (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36: W197-W201. doi:10.1093/nar/gkn238
    • (2008) Nucleic Acids Res , vol.36 , pp. W197-W201
    • Cole, C.1    Barber, J.D.2    Barton, G.J.3
  • 18
    • 0036763207 scopus 로고    scopus 로고
    • On filtering false positive transmembrane protein predictions
    • Cserzo M, Eisenhaber F, Eisenhaber B, Simon I (2002) On filtering false positive transmembrane protein predictions. Protein Eng 15:745-752
    • (2002) Protein Eng , vol.15 , pp. 745-752
    • Cserzo, M.1    Eisenhaber, F.2    Eisenhaber, B.3    Simon, I.4
  • 19
    • 0347093547 scopus 로고    scopus 로고
    • TM or not TM: Transmembrane protein prediction with low false positive rate using DAS-TMfilter
    • CserzoM, Eisenhaber F, Eisenhaber B, Simon I (2003)TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics 20:136-137. doi:10.1093/bioinformatics/btg394
    • (2003) Bioinformatics , vol.20 , pp. 136-137
    • Cserzo, M.1    Eisenhaber, F.2    Eisenhaber, B.3    Simon, I.4
  • 22
    • 79959959356 scopus 로고    scopus 로고
    • T-coffee: A web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
    • Di Tommaso P, Moretti S, Xenarios I et al (2011) T-coffee: A web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res 39: W13-W17. doi:10.1093/nar/gkr245
    • (2011) Nucleic Acids Res , vol.39 , pp. W13-W17
    • Di Tommaso, P.1    Moretti, S.2    Xenarios, I.3
  • 23
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do CB, Mahabhashyam MSP, Brudno M, Batzoglou S (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 15:330-340. doi:10.1101/gr.2821705
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.P.2    Brudno, M.3    Batzoglou, S.4
  • 24
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • Dosztányi Z, Csizmok V, Tompa P, Simon I (2005a) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21:3433-3434. doi:10.1093/bioinformatics/bti541
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztányi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 25
    • 14844342815 scopus 로고    scopus 로고
    • The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    • Dosztányi Z, Csizmók V, Tompa P, Simon I (2005b) The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 347:827-839. doi:10.1016/j.jmb.2005.01.071
    • (2005) J Mol Biol , vol.347 , pp. 827-839
    • Dosztányi, Z.1    Csizmók, V.2    Tompa, P.3    Simon, I.4
  • 26
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3. 0
    • Dyrlov Bendtsen J, Nielsen H, von Heijne G, Brunak Sa (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783-795. doi:10.1016/j. jmb.2004.05.028
    • (2004) J Mol Biol , vol.340 , pp. 783-795
    • Dyrlov Bendtsen, J.1    Nielsen, H.2    Von Heijne, G.3    Sa, B.4
  • 27
    • 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
  • 28
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7(10):e1002195
    • (2011) PLoS Comput Biol , vol.7 , Issue.10 , pp. e1002195
    • Eddy, S.R.1
  • 29
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar RC (2004a) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. doi:10.1186/1471-2105-5-113
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 30
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004b) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. doi:10.1093/nar/gkh340
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 32
    • 84864477028 scopus 로고    scopus 로고
    • A decade after the first full human genome sequencing:When will we understand our own genome?
    • Eisenhaber F (2012) A decade after the first full human genome sequencing:When will we understand our own genome? J Bioinformatics Comp Biol 10:1271001
    • (2012) J Bioinformatics Comp Biol , vol.10 , pp. 1271001
    • Eisenhaber, F.1
  • 33
    • 34247571020 scopus 로고    scopus 로고
    • Posttranslational modifications and subcellular localization signals: Indicators of sequence regions without inherent 3D structure?
    • Eisenhaber B, Eisenhaber F (2007) Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure? Curr Protein Pept Sci 8:197-203
    • (2007) Curr Protein Pept Sci , vol.8 , pp. 197-203
    • Eisenhaber, B.1    Eisenhaber, F.2
  • 34
    • 0029946575 scopus 로고    scopus 로고
    • Prediction of secondary structural content of proteins fromtheir aminoacid compositionalone. I. Newanalytic vector decomposition methods
    • Eisenhaber F, Imperiale F, Argos P, Frommel C (1996) Prediction of secondary structural content of proteins fromtheir aminoacid compositionalone. I.Newanalytic vector decomposition methods. Proteins 25:157-168. doi:10.1002/(SICI)1097-0134(199606)25:2<157::AID-PROT2>3.0.CO;2-F
    • (1996) Proteins , vol.25 , pp. 157-168
    • Eisenhaber, F.1    Imperiale, F.2    Argos, P.3    Frommel, C.4
  • 35
    • 0033600935 scopus 로고    scopus 로고
    • Prediction of potential GPI-modification sites in proprotein sequences
    • Eisenhaber B, Bork P, Eisenhaber F (1999) Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol 292:741-758. doi:10.1006/ jmbi.1999.3069
    • (1999) J Mol Biol , vol.292 , pp. 741-758
    • Eisenhaber, B.1    Bork, P.2    Eisenhaber, F.3
  • 36
    • 0037387522 scopus 로고    scopus 로고
    • Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins
    • EisenhaberB,Maurer-Stroh S,NovatchkovaMet al (2003a) Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins. Bioessays 25:367-385. doi:10.1002/bies.10254
    • (2003) Bioessays , vol.25 , pp. 367-385
    • Eisenhaber, B.1    Maurer-Stroh, S.2    Novatchkova, M.3
  • 37
    • 0043123048 scopus 로고    scopus 로고
    • Prediction of lipid posttranslational modifications and localization signals from protein sequences: Big-Pi, NMT and PTS1
    • Eisenhaber F, Eisenhaber B, Kubina W et al (2003b) Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Nucleic Acids Res 31:3631-3634
    • (2003) Nucleic Acids Res , vol.31 , pp. 3631-3634
    • Eisenhaber, F.1    Eisenhaber, B.2    Kubina, W.3
  • 38
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:1575-1584
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 39
    • 43749107283 scopus 로고    scopus 로고
    • Comparative protein structure modeling using Modeller
    • Unit 5.6 (Chap 5)
    • Eswar N, Webb B, Marti-Renom MA et al (2006) Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics Unit 5.6 (Chap 5). doi:10.1002/0471250953.bi0506s15
    • (2006) Curr Protoc Bioinformatics
    • Eswar, N.1    Webb, B.2    Marti-Renom, M.A.3
  • 40
    • 48849113878 scopus 로고    scopus 로고
    • Comparative protein structure modeling using MODELLER
    • Unit 2.9 (Chap 2)
    • Eswar N, Webb B, Marti-Renom MA et al (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci Unit 2.9 (Chap 2). doi:10.1002/0471140864.ps0209s50
    • (2007) Curr Protoc Protein Sci
    • Eswar, N.1    Webb, B.2    Marti-Renom, M.A.3
  • 41
    • 0032820595 scopus 로고    scopus 로고
    • The structure, biosynthesis and functions of glycosylphosphatidylinositol anchors, and the contributions of trypanosome research
    • Ferguson MA (1999) The structure, biosynthesis and functions of glycosylphosphatidylinositol anchors, and the contributions of trypanosome research. J Cell Sci 112(Pt 17):2799-2809
    • (1999) J Cell Sci , vol.112 , pp. 2799-2809
    • Ferguson, M.A.1
  • 42
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A, Do RK, Sali A (2000)Modeling of loops in protein structures. Protein Sci 9:1753-1773. doi:10.1110/ ps.9.9.1753
    • (2000) Protein Sci , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 43
    • 33947270331 scopus 로고    scopus 로고
    • MEL-28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly
    • Franz C,Walczak R, Yavuz S et al (2007)MEL-28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO Rep 8:165-172. doi:10.1038/sj.embor.7400889
    • (2007) EMBO Rep , vol.8 , pp. 165-172
    • Franz, C.1    Walczak, R.2    Yavuz, S.3
  • 44
    • 0029996162 scopus 로고    scopus 로고
    • Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence
    • Frishman D, Argos P (1996) Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng Des Sel 9:133-142. doi:10.1093/protein/9.2.133
    • (1996) Protein Eng des Sel , vol.9 , pp. 133-142
    • Frishman, D.1    Argos, P.2
  • 45
    • 0030931336 scopus 로고    scopus 로고
    • Seventy-five percent accuracy in protein secondary structure prediction
    • Frishman D, Argos P (1997) Seventy-five percent accuracy in protein secondary structure prediction. Proteins 27:329-335
    • (1997) Proteins , vol.27 , pp. 329-335
    • Frishman, D.1    Argos, P.2
  • 46
    • 33747827759 scopus 로고    scopus 로고
    • MEL-28, a novel nuclear-envelope and kinetochore protein essential for zygotic nuclear-envelope assembly in C
    • Galy V, Askjaer P, Franz C et al (2006) MEL-28, a novel nuclear-envelope and kinetochore protein essential for zygotic nuclear-envelope assembly in C. elegans. Curr Biol 16:1748-1756. doi:10.1016/j.cub.2006.06.067
    • (2006) Elegans. Curr Biol , vol.16 , pp. 1748-1756
    • Galy, V.1    Askjaer, P.2    Franz, C.3
  • 47
    • 77952136530 scopus 로고    scopus 로고
    • A draft sequence of the neandertal genome
    • Green RE, Krause J, Briggs AW et al (2010) A draft sequence of the neandertal genome. Science 328:710-722. doi:10.1126/science.1188021
    • (2010) Science , vol.328 , pp. 710-722
    • Green, R.E.1    Krause, J.2    Briggs, A.W.3
  • 48
    • 77957352833 scopus 로고    scopus 로고
    • Jmol-A paradigm shift in crystallographic visualization
    • Hanson RM (2010) Jmol-A paradigm shift in crystallographic visualization. J Appl Crystallogr 43:1250-1260. doi:10.1107/S0021889810030256
    • (2010) J Appl Crystallogr , vol.43 , pp. 1250-1260
    • Hanson, R.M.1
  • 50
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 51
  • 52
    • 0242458810 scopus 로고    scopus 로고
    • Order, disorder, and flexibility: Prediction from protein sequence
    • Iakoucheva LM, Dunker AK (2003) Order, disorder, and flexibility: prediction from protein sequence. Structure 11:1316-1317
    • (2003) Structure , vol.11 , pp. 1316-1317
    • Iakoucheva, L.M.1    Dunker, A.K.2
  • 53
    • 33751261643 scopus 로고    scopus 로고
    • Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer
    • Ivshina AV, George J, Senko O et al (2006) Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 66:10292-10301. doi:10.1158/0008-5472.CAN-05-4414
    • (2006) Cancer Res , vol.66 , pp. 10292-10301
    • Ivshina, A.V.1    George, J.2    Senko, O.3
  • 54
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide predictionmethod
    • Kall L, Krogh A, Sonnhammer ELL (2004) A combined transmembrane topology and signal peptide predictionmethod. J Mol Biol 338:1027-1036. doi:10.1016/j. jmb.2004.03.016
    • (2004) J Mol Biol , vol.338 , pp. 1027-1036
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 55
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh K (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511-518. doi:10.1093/nar/gki198
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1
  • 56
    • 33847310423 scopus 로고    scopus 로고
    • PartTree: An algorithm to build an approximate tree from a large number of unaligned sequences
    • Katoh K, Toh H (2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics 23:372-374. doi:10.1093/ bioinformatics/btl592
    • (2007) Bioinformatics , vol.23 , pp. 372-374
    • Katoh, K.1    Toh, H.2
  • 57
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:286-298. doi:10.1093/bib/bbn013
    • (2008) Brief Bioinform , vol.9 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 58
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Misawa K, K-ichi K, Miyata T (2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059-3066
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    K-Ichi, K.3    Miyata, T.4
  • 59
    • 79952140704 scopus 로고    scopus 로고
    • Judging the Archon Genomics X PRIZE for whole human genome sequencing
    • Kedes L, Liu E, Jongeneel CV, Sutton G (2011) Judging the Archon Genomics X PRIZE for whole human genome sequencing. Nat Genet 43:175. doi:10.1038/ ng0311-175
    • (2011) Nat Genet , vol.43 , pp. 175
    • Kedes, L.1    Liu, E.2    Jongeneel, C.V.3    Sutton, G.4
  • 60
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the web: A case study using the Phyre server
    • Kelley LA, Sternberg MJE (2009) Protein structure prediction on the web: A case study using the Phyre server. Nat Protoc 4:363-371. doi:10.1038/nprot.2009.2
    • (2009) Nat Protoc , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.E.2
  • 61
    • 33846047770 scopus 로고    scopus 로고
    • IntAct-open source resource for molecular interaction data
    • Kerrien S, Alam-Faruque Y, Aranda B et al (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35:D561-D565. doi:10.1093/nar/gkl958
    • (2007) Nucleic Acids Res , vol.35 , pp. D561-D565
    • Kerrien, S.1    Alam-Faruque, Y.2    Aranda, B.3
  • 62
    • 55049113078 scopus 로고    scopus 로고
    • Moore's law today
    • Keyes RW (2008) Moore's law today. IEEE Circuits Sys Mag 8:53-54. doi:10.1109/MCAS.2008.923058
    • (2008) IEEE Circuits Sys Mag , vol.8 , pp. 53-54
    • Keyes, R.W.1
  • 63
    • 0036235143 scopus 로고    scopus 로고
    • Identification of a novel transcription factor, ELYS, expressed predominantly in mouse foetal haematopoietic tissues
    • Kimura N, Takizawa M, Okita K et al (2002) Identification of a novel transcription factor, ELYS, expressed predominantly in mouse foetal haematopoietic tissues. Genes Cells 7:435-446
    • (2002) Genes Cells , vol.7 , pp. 435-446
    • Kimura, N.1    Takizawa, M.2    Okita, K.3
  • 64
    • 0035027535 scopus 로고    scopus 로고
    • An apology for orthologs-or brave new memes
    • Koonin EV (2001) An apology for orthologs-or brave new memes. Genome Biol 2:COMMENT1005
    • (2001) Genome Biol , vol.2
    • Koonin, E.V.1
  • 65
    • 0141738778 scopus 로고    scopus 로고
    • Comparison of sequence masking algorithms and the detection of biased protein sequence regions
    • Kreil DP, Ouzounis CA (2003) Comparison of sequence masking algorithms and the detection of biased protein sequence regions. Bioinformatics 19:1672-1681
    • (2003) Bioinformatics , vol.19 , pp. 1672-1681
    • Kreil, D.P.1    Ouzounis, C.A.2
  • 66
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567-580. doi:10.1006/ jmbi.2000.4315
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.4
  • 68
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander ES, Linton LM, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921. doi:10.1038/35057062
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1    Linton, L.M.2    Birren, B.3
  • 69
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast programfor clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A(2006)Cd-hit: A fast programfor clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659. doi:10.1093/ bioinformatics/btl158
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 70
    • 0035072551 scopus 로고    scopus 로고
    • Clustering of highly homologous sequences to reduce the size of large protein databases
    • Li W, Jaroszewski L, 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
  • 71
    • 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. doi:10.1093/bioinformatics/18.1.77
    • (2002) Bioinformatics , vol.18 , pp. 77-82
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 72
    • 0242458482 scopus 로고    scopus 로고
    • Protein disorder prediction
    • Linding R, Jensen LJ, Diella F et al (2003a) Protein disorder prediction. Structure 11:1453-1459. doi:10.1016/j. str.2003.10.002
    • (2003) Structure , vol.11 , pp. 1453-1459
    • Linding, R.1    Jensen, L.J.2    Diella, F.3
  • 73
    • 0042622240 scopus 로고    scopus 로고
    • GlobPlot: Exploring protein sequences for globularity and disorder
    • Linding R, Russell RB, Neduva V, Gibson TJ (2003b) 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
  • 74
    • 0030004228 scopus 로고    scopus 로고
    • Prediction and analysis of coiled-coil structures
    • Lupas A (1996) Prediction and analysis of coiled-coil structures. Meth Enzymol 266:513-525
    • (1996) Meth Enzymol , vol.266 , pp. 513-525
    • Lupas, A.1
  • 75
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas A, Van Dyke M, 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
  • 76
    • 78651285748 scopus 로고    scopus 로고
    • CDD: A conserved domain database for the functional annotation of proteins
    • Marchler-Bauer A, Lu S, Anderson JB et al (2011) CDD: A conserved domain database for the functional annotation of proteins. Nucleic Acids Res 39:D225-D229. doi:10.1093/nar/gkq1189
    • (2011) Nucleic Acids Res , vol.39 , pp. D225-D229
    • Marchler-Bauer, A.1    Lu, S.2    Anderson, J.B.3
  • 77
    • 0033873929 scopus 로고    scopus 로고
    • Comparative protein structure modeling of genes and genomes
    • Martí-Renom MA, Stuart AC, Fiser A et al (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291-325. doi:10.1146/annurev.biophys.29.1.291
    • (2000) Annu Rev Biophys Biomol Struct , vol.29 , pp. 291-325
    • Martí-Renom, M.A.1    Stuart, A.C.2    Fiser, A.3
  • 78
    • 1642340046 scopus 로고    scopus 로고
    • Myristoylation of viral and bacterial proteins
    • Maurer-Stroh S, Eisenhaber F (2004) Myristoylation of viral and bacterial proteins. Trends Microbiol 12:178-185. doi:10.1016/j.tim.2004.02.006
    • (2004) Trends Microbiol , vol.12 , pp. 178-185
    • Maurer-Stroh, S.1    Eisenhaber, F.2
  • 79
    • 33646366606 scopus 로고    scopus 로고
    • Refinement and prediction of protein prenylation motifs
    • Maurer-Stroh S, Eisenhaber F (2005) Refinement and prediction of protein prenylation motifs. Genome Biol 6:R55. doi:10.1186/gb-2005-6-6-r55
    • (2005) Genome Biol , vol.6 , pp. R55
    • Maurer-Stroh, S.1    Eisenhaber, F.2
  • 80
    • 0036290648 scopus 로고    scopus 로고
    • Nterminal N-myristoylation of proteins: Prediction of substrate proteins from amino acid sequence
    • Maurer-Stroh S, Eisenhaber B, Eisenhaber F (2002a) Nterminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J Mol Biol 317:541-557. doi:10.1006/jmbi.2002.5426
    • (2002) J Mol Biol , vol.317 , pp. 541-557
    • Maurer-Stroh, S.1    Eisenhaber, B.2    Eisenhaber, F.3
  • 81
    • 0036295384 scopus 로고    scopus 로고
    • Nterminal N-myristoylation of proteins: Refinement of the sequence motif and its taxon-specific differences
    • Maurer-Stroh S, Eisenhaber B, Eisenhaber F (2002b) Nterminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. J Mol Biol 317:523-540. doi:10.1006/jmbi.2002.5425
    • (2002) J Mol Biol , vol.317 , pp. 523-540
    • Maurer-Stroh, S.1    Eisenhaber, B.2    Eisenhaber, F.3
  • 82
    • 2942617973 scopus 로고    scopus 로고
    • MYRbase: Analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins
    • Maurer-Stroh S, Gouda M, Novatchkova M et al (2004) MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. Genome Biol 5:R21. doi:10.1186/gb-2004-5-3-r21
    • (2004) Genome Biol , vol.5 , pp. R21
    • Maurer-Stroh, S.1    Gouda, M.2    Novatchkova, M.3
  • 83
    • 34247648721 scopus 로고    scopus 로고
    • Towards complete sets of farnesylated and geranylgeranylated proteins
    • Maurer-Stroh S, Koranda M, Benetka W et al (2007) Towards complete sets of farnesylated and geranylgeranylated proteins. PLoS Comput Biol 3:e66. doi:10.1371/journal.pcbi.0030066
    • (2007) PLoS Comput Biol , vol.3 , pp. e66
    • Maurer-Stroh, S.1    Koranda, M.2    Benetka, W.3
  • 84
    • 67749114646 scopus 로고    scopus 로고
    • Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites
    • discussion 18
    • Maurer-Stroh S, Ma J, Lee RTC, et al. (2009) Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites. Biol Direct 4:18; discussion 18. doi:10.1186/1745-6150-4-18
    • (2009) Biol Direct , vol.4 , pp. 18
    • Maurer-Stroh, S.1    Ma, J.2    Lee, R.T.C.3
  • 86
    • 1242339659 scopus 로고    scopus 로고
    • A family of evolution-entropy hybrid methods for ranking protein residues by importance
    • Mihalek I, Res I, Lichtarge O (2004) A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol 336:1265-1282. doi:10.1016/j.jmb.2003.12.078
    • (2004) J Mol Biol , vol.336 , pp. 1265-1282
    • Mihalek, I.1    Res, I.2    Lichtarge, O.3
  • 87
    • 0034054666 scopus 로고    scopus 로고
    • Molecular and functional properties of the human alpha(1 G) subunit that forms T-type calcium channels
    • Monteil A, Chemin J, Bourinet E et al (2000a) Molecular and functional properties of the human alpha(1 G) subunit that forms T-type calcium channels. J Biol Chem 275:6090-6100
    • (2000) J Biol Chem , vol.275 , pp. 6090-6100
    • Monteil, A.1    Chemin, J.2    Bourinet, E.3
  • 88
    • 0034595807 scopus 로고    scopus 로고
    • Specific properties of T-type calcium channels generated by the human alpha 1I subunit
    • Monteil A, Chemin J, Leuranguer V et al (2000b) Specific properties of T-type calcium channels generated by the human alpha 1I subunit. J Biol Chem 275:16530-16535. doi:10.1074/jbc.C000090200
    • (2000) J Biol Chem , vol.275 , pp. 16530-16535
    • Monteil, A.1    Chemin, J.2    Leuranguer, V.3
  • 89
    • 0034647416 scopus 로고    scopus 로고
    • Accurate formula for P-values of gapped local sequence and profile alignments
    • Mott R (2000) Accurate formula for P-values of gapped local sequence and profile alignments. J Mol Biol 300:649-659. doi:10.1006/jmbi.2000.3875
    • (2000) J Mol Biol , vol.300 , pp. 649-659
    • Mott, R.1
  • 90
    • 0012302769 scopus 로고    scopus 로고
    • An integrated computational pipeline and database to support whole-genome sequence annotation
    • Mungall CJ, Misra S, Berman BP et al (2002) An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol 3:RESEARCH0081
    • (2002) Genome Biol , vol.3
    • Mungall, C.J.1    Misra, S.2    Berman, B.P.3
  • 91
    • 0037414458 scopus 로고    scopus 로고
    • Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence
    • Neuberger G, Maurer-Stroh S, Eisenhaber B et al (2003a) Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. J Mol Biol 328:581-592
    • (2003) J Mol Biol , vol.328 , pp. 581-592
    • Neuberger, G.1    Maurer-Stroh, S.2    Eisenhaber, B.3
  • 92
    • 0037414447 scopus 로고    scopus 로고
    • Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences
    • Neuberger G, Maurer-Stroh S, Eisenhaber B et al (2003b) Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences. J Mol Biol 328:567-579
    • (2003) J Mol Biol , vol.328 , pp. 567-579
    • Neuberger, G.1    Maurer-Stroh, S.2    Eisenhaber, B.3
  • 93
    • 0031603460 scopus 로고    scopus 로고
    • Prediction of signal peptides and signal anchors by a hidden Markov model
    • Nielsen H, Krogh A (1998) Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol 6:122-130
    • (1998) Proc Int Conf Intell Syst Mol Biol , vol.6 , pp. 122-130
    • Nielsen, H.1    Krogh, A.2
  • 94
    • 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 Eng 10:1-6
    • (1997) Protein Eng , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    Von Heijne, G.4
  • 95
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205-217. doi:10.1006/jmbi.2000.4042
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 96
    • 33747825726 scopus 로고    scopus 로고
    • DOUTfinder-identification of distant domain outliers using subsignificant sequence similarity
    • Novatchkova M, Schneider G, Fritz R et al (2006) DOUTfinder-identification of distant domain outliers using subsignificant sequence similarity. Nucleic Acids Res 34:W214-W218. doi:10.1093/nar/gkl332
    • (2006) Nucleic Acids Res , vol.34 , pp. W214-W218
    • Novatchkova, M.1    Schneider, G.2    Fritz, R.3
  • 97
    • 7944221427 scopus 로고    scopus 로고
    • Targeted disruption of the mouse ELYS gene results in embryonic death at peri-implantation development
    • Okita K, Kiyonari H, Nobuhisa I et al (2004) Targeted disruption of the mouse ELYS gene results in embryonic death at peri-implantation development. Genes Cells 9:1083-1091. doi:10.1111/j.1365-2443.2004.00791.x
    • (2004) Genes Cells , vol.9 , pp. 1083-1091
    • Okita, K.1    Kiyonari, H.2    Nobuhisa, I.3
  • 98
    • 67749125573 scopus 로고    scopus 로고
    • ANNIE: Integrated de novo protein sequence annotation
    • Ooi HS, Kwo CY, Wildpaner M et al (2009) ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res 37:W435-W440. doi:10.1093/nar/gkp254
    • (2009) Nucleic Acids Res , vol.37 , pp. W435-W440
    • Ooi, H.S.1    Kwo, C.Y.2    Wildpaner, M.3
  • 99
    • 77952778487 scopus 로고    scopus 로고
    • Databases of protein-protein interactions and complexes
    • Ooi HS, Schneider G, Chan Y-L et al (2010a) Databases of protein-protein interactions and complexes. Methods Mol Biol 609:145-159. doi:10.1007/978-1-60327-241-4-9
    • (2010) Methods Mol Biol , vol.609 , pp. 145-159
    • Ooi, H.S.1    Schneider, G.2    Chan, Y.-L.3
  • 100
    • 77952773735 scopus 로고    scopus 로고
    • Biomolecular pathway databases
    • Ooi HS, Schneider G, Lim T-T et al (2010b) Biomolecular pathway databases. Methods Mol Biol 609:129-144. doi:10.1007/978-1-60327-241-4-8
    • (2010) Methods Mol Biol , vol.609 , pp. 129-144
    • Ooi, H.S.1    Schneider, G.2    Lim, T.-T.3
  • 101
    • 0037462424 scopus 로고    scopus 로고
    • Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase
    • Orlicky S, Tang X, Willems A et al (2003) Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase. Cell 112:243-256
    • (2003) Cell , vol.112 , pp. 243-256
    • Orlicky, S.1    Tang, X.2    Willems, A.3
  • 102
    • 0034604451 scopus 로고    scopus 로고
    • Crystal structure of rhodopsin: A G protein-coupled receptor
    • Palczewski K, Kumasaka T, Hori T et al (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289:739-745. doi:10.1126/science.289.5480.739
    • (2000) Science , vol.289 , pp. 739-745
    • Palczewski, K.1    Kumasaka, T.2    Hori, T.3
  • 103
    • 0032509105 scopus 로고    scopus 로고
    • Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
    • Park J, Karplus K, Barrett C et al (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 284:1201-1210. doi:10.1006/jmbi.1998.2221
    • (1998) J Mol Biol , vol.284 , pp. 1201-1210
    • Park, J.1    Karplus, K.2    Barrett, C.3
  • 104
    • 0032512799 scopus 로고    scopus 로고
    • Empirical statistical estimates for sequence similarity searches
    • Pearson WR (1998) Empirical statistical estimates for sequence similarity searches. J Mol Biol 276:71-84. doi:10.1006/jmbi.1997.1525
    • (1998) J Mol Biol , vol.276 , pp. 71-84
    • Pearson, W.R.1
  • 105
    • 0033990061 scopus 로고    scopus 로고
    • Flexible sequence similarity searching with the FASTA3 program package
    • Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 132:185-219
    • (2000) Methods Mol Biol , vol.132 , pp. 185-219
    • Pearson, W.R.1
  • 106
    • 34548573170 scopus 로고    scopus 로고
    • Why are there still over 1000 uncharacterized yeast genes?
    • Penã-Castillo L, Hughes TR (2007) Why are there still over 1000 uncharacterized yeast genes? Genetics 176:7-14. doi:10.1534/genetics.107.074468
    • (2007) Genetics , vol.176 , pp. 7-14
    • Penã-Castillo, L.1    Hughes, T.R.2
  • 107
    • 0037274724 scopus 로고    scopus 로고
    • Betapropellers: Associated functions and their role in human diseases
    • Pons T, Gómez R, Chinea G, Valencia A (2003) Betapropellers: associated functions and their role in human diseases. Curr Med Chem 10:505-524
    • (2003) Curr Med Chem , vol.10 , pp. 505-524
    • Pons, T.1    Gómez, R.2    Chinea, G.3    Valencia, A.4
  • 108
    • 0033638015 scopus 로고    scopus 로고
    • CAST: An iterative algorithmfor the complexity analysis of sequence tracts
    • Promponas VJ, Enright AJ, Tsoka S et al (2000) CAST: an iterative algorithmfor the complexity analysis of sequence tracts. Bioinformatics 16:915-922. doi:10.1093/bioinformatics/ 16.10.915
    • (2000) Bioinformatics , vol.16 , pp. 915-922
    • Promponas, V.J.1    Enright, A.J.2    Tsoka, S.3
  • 109
    • 0042622252 scopus 로고    scopus 로고
    • ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
    • Puntervoll P, Linding R, Gemund C et al (2003) ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 31:3625-3630
    • (2003) Nucleic Acids Res , vol.31 , pp. 3625-3630
    • Puntervoll, P.1    Linding, R.2    Gemund, C.3
  • 110
    • 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 et al (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18:S71
    • (2002) Bioinformatics , vol.18 , pp. S71
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3
  • 111
    • 33845227470 scopus 로고    scopus 로고
    • ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division
    • Rasala BA, Orjalo AV, Shen Z et al (2006) ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division. Proc Natl Acad Sci USA 103:17801-17806. doi:10.1073/ pnas.0608484103
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 17801-17806
    • Rasala, B.A.1    Orjalo, A.V.2    Shen, Z.3
  • 112
    • 55549131172 scopus 로고    scopus 로고
    • Capture of AT-rich chromatin by ELYS recruits POM121 and NDC1 to initiate nuclear pore assembly
    • Rasala BA, Ramos C, Harel A, Forbes DJ (2008) Capture of AT-rich chromatin by ELYS recruits POM121 and NDC1 to initiate nuclear pore assembly. Mol Biol Cell 19:3982-3996. doi:10.1091/mbc.E08-01-0012
    • (2008) Mol Biol Cell , vol.19 , pp. 3982-3996
    • Rasala, B.A.1    Ramos, C.2    Harel, A.3    Forbes, D.J.4
  • 113
    • 0033794367 scopus 로고    scopus 로고
    • High-throughput protein crystallization
    • Raymond CS (2000) High-throughput protein crystallization. Curr Opin Struct Biol 10:558-563. doi:10.1016/ S0959-440X(00)00131-7
    • (2000) Curr Opin Struct Biol , vol.10 , pp. 558-563
    • Raymond, C.S.1
  • 114
    • 59149097358 scopus 로고    scopus 로고
    • Algorithm of OMA for large-scale orthology inference
    • Roth AC, Gonnet GH, Dessimoz C (2008) Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics 9:518. doi:10.1186/1471-2105-9-518
    • (2008) BMC Bioinformatics , vol.9 , pp. 518
    • Roth, A.C.1    Gonnet, G.H.2    Dessimoz, C.3
  • 115
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815. doi:10.1006/jmbi.1993.1626
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 116
    • 0038438514 scopus 로고    scopus 로고
    • IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    • Schaffer AA, Wolf YI, Ponting CP et al (1999) IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 15:1000-1011
    • (1999) Bioinformatics , vol.15 , pp. 1000-1011
    • Schaffer, A.A.1    Wolf, Y.I.2    Ponting, C.P.3
  • 117
    • 33645788381 scopus 로고    scopus 로고
    • Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases
    • Schneider G, Neuberger G, Wildpaner M et al (2006) Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. BMC Bioinformatics 7:164. doi:10.1186/1471-2105-7-164
    • (2006) BMC Bioinformatics , vol.7 , pp. 164
    • Schneider, G.1    Neuberger, G.2    Wildpaner, M.3
  • 118
    • 77952786465 scopus 로고    scopus 로고
    • Integrated tools for biomolecular sequence-based function prediction as exemplified by the ANNOTATOR software environment
    • Schneider G, Wildpaner M, Sirota FL et al (2010) Integrated tools for biomolecular sequence-based function prediction as exemplified by the ANNOTATOR software environment. Methods Mol Biol 609:257-267. doi:10.1007/978-1-60327-241-4-15
    • (2010) Methods Mol Biol , vol.609 , pp. 257-267
    • Schneider, G.1    Wildpaner, M.2    Sirota, F.L.3
  • 119
    • 25644451272 scopus 로고    scopus 로고
    • Correcting BLAST e-values for low-complexity segments
    • Sharon I, Birkland A, Chang K et al (2005) Correcting BLAST e-values for low-complexity segments. J Comput Biol 12:980-1003. doi:10.1089/cmb.2005.12.980
    • (2005) J Comput Biol , vol.12 , pp. 980-1003
    • Sharon, I.1    Birkland, A.2    Chang, K.3
  • 120
    • 0001290045 scopus 로고    scopus 로고
    • PROSITE: A documented database using patterns and profiles as motif descriptors
    • Sigrist CJA, Cerutti L, Hulo N et al (2002) PROSITE: A documented database using patterns and profiles as motif descriptors. Brief Bioinformatics 3:265-274
    • (2002) Brief Bioinformatics , vol.3 , pp. 265-274
    • Sigrist, C.J.A.1    Cerutti, L.2    Hulo, N.3
  • 121
    • 76749161891 scopus 로고    scopus 로고
    • Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset
    • Sirota FL, Ooi H-S, Gattermayer T et al (2010) Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset. BMC Genomics 11:S15. doi:10. 1186/1471-2164-11-S1-S15
    • (2010) BMC Genomics , vol.11 , pp. S15
    • Sirota, F.L.1    Ooi, H.-S.2    Gattermayer, T.3
  • 122
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMMHMM comparison
    • Soding J (2005) Protein homology detection by HMMHMM comparison. Bioinformatics 21:951-960. doi:10.1093/bioinformatics/bti125
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 123
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244-W248. doi:10.1093/nar/gki408
    • (2005) Nucleic Acids Res , vol.33 , pp. W244-W248
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 124
  • 125
    • 34347388470 scopus 로고    scopus 로고
    • UniRef: Comprehensive and non-redundant UniProt reference clusters
    • Suzek BE, Huang H, McGarvey P et al (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23:1282
    • (2007) Bioinformatics , vol.23 , pp. 1282
    • Suzek, B.E.1    Huang, H.2    McGarvey, P.3
  • 127
    • 0032561132 scopus 로고    scopus 로고
    • Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
    • Tusnády GE, Simon I (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 283:489-506. doi:10.1006/jmbi.1998.2107
    • (1998) J Mol Biol , vol.283 , pp. 489-506
    • Tusnády, G.E.1    Simon, I.2
  • 128
    • 61849113253 scopus 로고    scopus 로고
    • Graph clustering via a discrete uncoupling process
    • Van Dongen S (2008) Graph clustering via a discrete uncoupling process. SIAM J Matrix Anal Appl 30:121. doi:10.1137/040608635
    • (2008) SIAM J Matrix Anal Appl , vol.30 , pp. 121
    • Van Dongen, S.1
  • 129
    • 0023046815 scopus 로고
    • A new method for predicting signal sequence cleavage sites
    • von Heijne G (1986) A new method for predicting signal sequence cleavage sites. Nucleic Acids Res 14:4683-4690. doi:10.1093/nar/14.11.4683
    • (1986) Nucleic Acids Res , vol.14 , pp. 4683-4690
    • Von Heijne, G.1
  • 130
    • 0026716643 scopus 로고
    • Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
    • von Heijne G (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225:487-494
    • (1992) J Mol Biol , vol.225 , pp. 487-494
    • Von Heijne, G.1
  • 131
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin E, von Heijne G (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7:1029-1038. doi:10.1002/pro.5560070420
    • (1998) Protein Sci , vol.7 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 132
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
    • Ward JJ, Sodhi JS, McGuffin LJ et al (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337:635-645. doi:10.1016/j.jmb.2004.02.002
    • (2004) J Mol Biol , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    McGuffin, L.J.3
  • 133
    • 47949129742 scopus 로고    scopus 로고
    • Structure of a [bgr]1-adrenergic G-protein-coupled receptor
    • Warne T, Serrano-Vega MJ, Baker JG et al (2008) Structure of a [bgr]1-adrenergic G-protein-coupled receptor. Nature 454:486-491. doi:10.1038/nature07101
    • (2008) Nature , vol.454 , pp. 486-491
    • Warne, T.1    Serrano-Vega, M.J.2    Baker, J.G.3
  • 134
    • 65449188232 scopus 로고    scopus 로고
    • Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    • Waterhouse AM, Procter JB, Martin DMA et al (2009) Jalview Version 2-A multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189-1191. doi:10.1093/bioinformatics/btp033
    • (2009) Bioinformatics , vol.25 , pp. 1189-1191
    • Waterhouse, A.M.1    Procter, J.B.2    Martin, D.M.A.3
  • 135
    • 69849086706 scopus 로고    scopus 로고
    • Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element
    • Whittle JRR, Schwartz TU (2009) Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element. J Biol Chem 284:28442-28452. doi:10.1074/jbc. M109.023580
    • (2009) J Biol Chem , vol.284 , pp. 28442-28452
    • Whittle, J.R.R.1    Schwartz, T.U.2
  • 136
    • 0033008596 scopus 로고    scopus 로고
    • Distribution of protein folds in the three superkingdoms of life
    • Wolf YI, Brenner SE, Bash PA, Koonin EV (1999) Distribution of protein folds in the three superkingdoms of life. Genome Res 9:17-26
    • (1999) Genome Res , vol.9 , pp. 17-26
    • Wolf, Y.I.1    Brenner, S.E.2    Bash, P.A.3    Koonin, E.V.4
  • 137
    • 78049250483 scopus 로고    scopus 로고
    • More than 1,001 problems with protein domain databases: Transmembrane regions, signal peptides and the issue of sequence homology
    • Wong W-C, Maurer-Stroh S, Eisenhaber F (2010) More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PLoS Comput Biol 6: e1000867. doi:10.1371/journal.pcbi.1000867
    • (2010) PLoS Comput Biol , vol.6 , pp. e1000867
    • Wong, W.-C.1    Maurer-Stroh, S.2    Eisenhaber, F.3
  • 138
    • 79851508880 scopus 로고    scopus 로고
    • The Janus-faced E-values of HMMER2: Extreme value distribution or logistic function?
    • Wong W-C, Maurer-Stroh S, Eisenhaber F (2011a) The Janus-faced E-values of HMMER2: extreme value distribution or logistic function? J Bioinform Comput Biol 9:179-206
    • (2011) J Bioinform Comput Biol , vol.9 , pp. 179-206
    • Wong, W.-C.1    Maurer-Stroh, S.2    Eisenhaber, F.3
  • 139
    • 80054826091 scopus 로고    scopus 로고
    • Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins
    • Wong W-C, Maurer-Stroh S, Eisenhaber F (2011b) Not all transmembrane helices are born equal: towards the extension of the sequence homology concept to membrane proteins. Biol Direct 6:57. doi:10.1186/1745-6150-6-57
    • (2011) Biol Direct , vol.6 , pp. 57
    • Wong, W.-C.1    Maurer-Stroh, S.2    Eisenhaber, F.3
  • 140
    • 0028501914 scopus 로고
    • Non-globular domains in protein sequences: Automated segmentation using complexity measures
    • Wootton JC (1994a) Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 18:269-285
    • (1994) Comput Chem , vol.18 , pp. 269-285
    • Wootton, J.C.1
  • 141
    • 0028234347 scopus 로고
    • Sequences with "unusual" amino acid compositions
    • Wootton JC (1994b) Sequences with "unusual" amino acid compositions. Curr Opin Struct Biol 4:413-421. doi:10.1016/S0959-440X(94)90111-2
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 413-421
    • Wootton, J.C.1
  • 142
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Wootton JC, Federhen S (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput Chem 17:149-163. doi:10.1016/0097-8485(93)85006-X
    • (1993) Comput Chem , vol.17 , pp. 149-163
    • Wootton, J.C.1    Federhen, S.2
  • 143
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootton JC, Federhen S (1996) Analysis of compositionally biased regions in sequence databases. Methods in Enzymology 266:554-571
    • (1996) Methods in Enzymology , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 144
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios I, Salwínski L, Duan XJ et al (2002) DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30:303-305
    • (2002) Nucleic Acids Res , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwínski, L.2    Duan, X.J.3
  • 145
    • 0035461311 scopus 로고    scopus 로고
    • ATP synthase-A marvellous rotary engine of the cell
    • Yoshida M, Muneyuki E, Hisabori T (2001) ATP synthase-A marvellous rotary engine of the cell. Nat Rev Mol Cell Biol 2:669-677. doi:10.1038/35089509
    • (2001) Nat Rev Mol Cell Biol , vol.2 , pp. 669-677
    • Yoshida, M.1    Muneyuki, E.2    Hisabori, T.3


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