메뉴 건너뛰기




Volumn 10, Issue 10, 2015, Pages

Computational identification of MoRFs in protein sequences using Hierarchical application of bayes rule

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; CONTROLLED STUDY; MOLECULAR RECOGNITION; PHOTOSYSTEM I; PLANT LEAF; PREDICTION; PROPENSITY SCORE; VELOCITY; BAYES THEOREM; BIOLOGY; CHEMISTRY; GENETICS; HUMAN; METABOLISM; PROCEDURES; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

EID: 84951014813     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0141603     Document Type: Article
Times cited : (37)

References (33)
  • 1
    • 84902446851 scopus 로고    scopus 로고
    • Classification of intrinsically disordered regions and proteins
    • Jul 9 PMID: 24773235
    • Van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, et al. Classification of intrinsically disordered regions and proteins. Chem Rev. 2014 Jul 9; 114(13):6589-631. doi: 10.1021/cr400525m PMID: 24773235
    • (2014) Chem Rev. , vol.114 , Issue.13 , pp. 6589-6631
    • Van Der Lee, R.1    Buljan, M.2    Lang, B.3    Weatheritt, R.J.4    Daughdrill, G.W.5    Dunker, A.K.6
  • 2
    • 84902160274 scopus 로고    scopus 로고
    • Intrinsically disordered proteins and intrinsically disordered protein regions
    • PMID: 24606139
    • Oldfield CJ, Dunker AK. Intrinsically disordered proteins and intrinsically disordered protein regions. Annu Rev Biochem. 2014; 83:553-84. doi: 10.1146/annurev-biochem-072711-164947 PMID: 24606139
    • (2014) Annu Rev Biochem. , vol.83 , pp. 553-584
    • Oldfield, C.J.1    Dunker, A.K.2
  • 3
    • 84925114160 scopus 로고    scopus 로고
    • Intrinsically disordered proteins in cellular signalling and regulation
    • Jan PMID: 25531225
    • Wright PE, Dyson HJ. Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol. 2015 Jan; 16(1):18-29. doi: 10.1038/nrm3920 PMID: 25531225
    • (2015) Nat Rev Mol Cell Biol. , vol.16 , Issue.1 , pp. 18-29
    • Wright, P.E.1    Dyson, H.J.2
  • 4
    • 84883419186 scopus 로고    scopus 로고
    • Promiscuity as a functional trait: Intrinsically disordered regions as central players of interactomes
    • Sep 15 PMID: 23988124
    • Cumberworth A, Lamour G, Babu MM and Gsponer J. Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes. Biochem. J., 2013 Sep 15; 454, 361-369. doi: 10. 1042/BJ20130545 PMID: 23988124
    • (2013) Biochem. J. , vol.454 , pp. 361-369
    • Cumberworth, A.1    Lamour, G.2    Babu, M.M.3    Gsponer, J.4
  • 6
    • 24944546549 scopus 로고    scopus 로고
    • Coupled folding and binding with alpha-helix-forming molecular recognition elements
    • PMID: 16156658
    • Oldfield CJ, Cheng Y, Cortese MS, Romero P, Uversky VN, Dunker AK. Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry, 44 (2005), pp. 12454-12470. PMID: 16156658
    • (2005) Biochemistry , vol.44 , pp. 12454-12470
    • Oldfield, C.J.1    Cheng, Y.2    Cortese, M.S.3    Romero, P.4    Uversky, V.N.5    Dunker, A.K.6
  • 8
    • 36749037699 scopus 로고    scopus 로고
    • Mining alpha-helix-forming molecular recognition features with cross species sequence alignments
    • Nov 27 PMID: 17973494
    • Cheng Y, Oldfield CJ, Meng J, Romero P, Uversky VN, Dunker AK. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry. 2007 Nov 27; 46 (47):13468-77. PMID: 17973494
    • (2007) Biochemistry. , vol.46 , Issue.47 , pp. 13468-13477
    • Cheng, Y.1    Oldfield, C.J.2    Meng, J.3    Romero, P.4    Uversky, V.N.5    Dunker, A.K.6
  • 10
    • 84883313748 scopus 로고    scopus 로고
    • On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins
    • Aug 22 PMID: 23990768
    • Wong ETC, NAD, Gsponer J. On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins. PLoS Comput Biol, 2013 Aug 22; 9(8), e1003192. doi: 10.1371/journal. pcbi.1003192 PMID: 23990768
    • (2013) PLoS Comput Biol , vol.9 , Issue.8 , pp. e1003192
    • Etc, W.1    Nad Gsponer, J.2
  • 11
    • 84862992463 scopus 로고    scopus 로고
    • Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks
    • Jun 29; PMID: 22749400
    • Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, et al. Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks. Mol Cell. 2012 Jun 29; 46(6):871-83. doi: 10.1016/j.molcel.2012.05.039 PMID: 22749400
    • (2012) Mol Cell. , vol.46 , Issue.6 , pp. 871-883
    • Buljan, M.1    Chalancon, G.2    Eustermann, S.3    Wagner, G.P.4    Fuxreiter, M.5    Bateman, A.6
  • 12
    • 67049119327 scopus 로고    scopus 로고
    • Prediction of protein binding regions in disordered proteins
    • May 1; PMID: 19412530
    • Mészáros B, Simon I, Dosztányi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol., 2009 May 1; 5, e1000376. doi: 10.1371/journal.pcbi.1000376 PMID: 19412530
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000376
    • Mészáros, B.1    Simon, I.2    Dosztányi, Z.3
  • 13
    • 84863518014 scopus 로고    scopus 로고
    • MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins
    • Jun 15; PMID: 22689782
    • Disfani FM, Hsu WL, Mizianty MJ, Oldfield CJ, Xue B, Dunker AK, et al. MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics, 2012 Jun 15; 28 (12): i75-i83. doi: 10.1093/bioinformatics/bts209 PMID: 22689782
    • (2012) Bioinformatics , vol.28 , Issue.12 , pp. i75-i83
    • Disfani, F.M.1    Hsu, W.L.2    Mizianty, M.J.3    Oldfield, C.J.4    Xue, B.5    Dunker, A.K.6
  • 14
    • 84884959977 scopus 로고    scopus 로고
    • MFSPSSMpred: Identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation
    • Oct 4; PMID: 24093637
    • Fang C, Noguchi T, Tominaga D and Yamana H. MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation. BMC Bioinformatics, 2013 Oct 4; 14:300 doi: 10.1186/1471-2105-14-300 PMID: 24093637
    • (2013) BMC Bioinformatics , vol.14 , pp. 300
    • Fang, C.1    Noguchi, T.2    Tominaga, D.3    Yamana, H.4
  • 15
    • 84925251625 scopus 로고    scopus 로고
    • DISOPRED3: Precise disordered region predictions with annotated protein-binding activity
    • Mar 15; PMID: 25391399
    • Jones DT and Cozzetto D. DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics, 2015 Mar 15; 31 (6): 857-863. doi: 10.1093/bioinformatics/btu744 PMID: 25391399
    • (2015) Bioinformatics , vol.31 , Issue.6 , pp. 857-863
    • Jones, D.T.1    Cozzetto, D.2
  • 16
    • 84934959184 scopus 로고    scopus 로고
    • Computational Identification of MoRFs in Protein Sequences
    • Jan 30; PMID: 25637562
    • Malhis N and Gsponer J. Computational Identification of MoRFs in Protein Sequences. Bioinformatics 2015 Jan 30; 31 (11): 1738-1744. doi: 10.1093/bioinformatics/btv060 PMID: 25637562
    • (2015) Bioinformatics , vol.31 , Issue.11 , pp. 1738-1744
    • Malhis, N.1    Gsponer, J.2
  • 17
    • 77949916296 scopus 로고    scopus 로고
    • Understanding protein non-folding
    • Jun 1; PMID: 20117254
    • Uversky VN, and Dunker AK. Understanding protein non-folding. Biochim Biophys Acta. 2010 Jun 1; 1804 (6):1231-64. doi: 10.1016/j.bbapap.2010.01.017 PMID: 20117254
    • (2010) Biochim Biophys Acta. , vol.1804 , Issue.6 , pp. 1231-1264
    • Uversky, V.N.1    Dunker, A.K.2
  • 18
    • 34547943482 scopus 로고    scopus 로고
    • Molecular Principles of the Interactions of Disordered Proteins
    • Sep 14
    • Mészáros B, Tompa P, Simon I and Dosztányi Z. Molecular Principles of the Interactions of Disordered Proteins. JMB, 2007 Sep 14; Volume 372, Issue 2, Pages 549-561.
    • (2007) JMB , vol.372 , Issue.2 , pp. 549-561
    • Mészáros, B.1    Tompa, P.2    Simon, I.3    Dosztányi, Z.4
  • 19
    • 84874828251 scopus 로고    scopus 로고
    • Structure and Intrinsic Disorder in Protein Autoinhibition
    • Mar 5; PMID: 23375259
    • Trudeau T, Nassar R, Cumberworth A, Wong ETC, Woollard G and Gsponer J. Structure and Intrinsic Disorder in Protein Autoinhibition. STRUCTURE 2013 Mar 5; 21, 332-341. doi: 10.1016/j.str.2012.12. 013 PMID: 23375259
    • (2013) STRUCTURE , vol.21 , pp. 332-341
    • Trudeau, T.1    Nassar, R.2    Cumberworth, A.3    Etc, W.4    Woollard, G.5    Gsponer, J.6
  • 20
    • 3242891318 scopus 로고    scopus 로고
    • The DISOPRED server for the prediction of protein disorder
    • PMID: 15044227
    • Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT. The DISOPRED server for the prediction of protein disorder. Bioinformatics, 2004; 20, 2138-2139. PMID: 15044227
    • (2004) Bioinformatics , vol.20 , pp. 2138-2139
    • Ward, J.J.1    McGuffin, L.J.2    Bryson, K.3    Buxton, B.F.4    Jones, D.T.5
  • 21
    • 84857170967 scopus 로고    scopus 로고
    • ESpritz: Accurate and fast prediction of protein disorder
    • PMID: 22190692
    • Walsh I, Martin AJ, Di Domenico T, Tosatto SC. ESpritz: accurate and fast prediction of protein disorder. Bioinformatics. 2012; 28(4):503-9. doi: 10.1093/bioinformatics/btr682 PMID: 22190692
    • (2012) Bioinformatics. , vol.28 , Issue.4 , pp. 503-509
    • Walsh, I.1    Martin, A.J.2    Di Domenico, T.3    Tosatto, S.C.4
  • 22
    • 14844342815 scopus 로고    scopus 로고
    • The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    • Apr 8 PMID: 15769473
    • Dosztányi Z, Csizmók V, Tompa P, Simon I. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 2005 Apr 8; 347: 827-839. PMID: 15769473
    • (2005) J Mol Biol , vol.347 , pp. 827-839
    • Dosztányi, Z.1    Csizmók, V.2    Tompa, P.3    Simon, I.4
  • 23
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: Web serverforthe prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • Aug 15; PMID: 15955779
    • Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web serverforthe prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005 Aug 15; 21 (16):3433-4. PMID: 15955779
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3433-3434
    • Dosztányi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 24
    • 84855184716 scopus 로고    scopus 로고
    • SPINE-D: Accurate prediction of short and long disordered regions by a single neural-network based method
    • PMID: 22208280
    • Zhang T, Faraggi E, Xue B, Dunker AK, Uversky VN, Zhou Y. SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. J Biomol Struct Dyn. 2012; 29 (4):799-813. PMID: 22208280
    • (2012) J Biomol Struct Dyn. , vol.29 , Issue.4 , pp. 799-813
    • Zhang, T.1    Faraggi, E.2    Xue, B.3    Dunker, A.K.4    Uversky, V.N.5    Zhou, Y.6
  • 25
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Sep 1 PMID: 9254694
    • Altschul SF, Madden TL, SchäfferAA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 1997 Sep 1; 25(17), 3389-3402. PMID: 9254694
    • (1997) Nucl. Acids Res. , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäfferaa Zhang, J.3    Zhang, Z.4    Miller, W.5
  • 26
    • 0036495004 scopus 로고    scopus 로고
    • Getting the most from PSI-BLAST
    • Mar PMID: 11893514
    • Jones DT, Swindells MB. Getting the most from PSI-BLAST. Trends Biochem. Sci. 2002 Mar; 27, 161-164. PMID: 11893514
    • (2002) Trends Biochem. Sci. , vol.27 , pp. 161-164
    • Jones, D.T.1    Swindells, M.B.2
  • 28
    • 84863304598 scopus 로고    scopus 로고
    • R Core Team ( R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
    • R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. Available: http://www.R-project.org/.
    • (2013) R: A Language and Environment for Statistical Computing
  • 29
    • 0003742069 scopus 로고
    • (Department of Biochemistry and Molecular Biology University College London).
    • Hubbard SJ, Thornton JM, 'NACCESS', Computer Program (Department of Biochemistry and Molecular Biology, University College London). 1993. Available: http://www.bioinf.manchester.ac.uk/naccess/.
    • (1993) 'Naccess', Computer Program
    • Hubbard, S.J.1    Thornton, J.M.2
  • 30
    • 84864311086 scopus 로고    scopus 로고
    • Linear motifs: Lost in (pre)translation
    • August PMID: 22705166
    • Weatheritt R.J. and Gibson T.J. Linear motifs: lost in (pre)translation. Trends in Biochemical Sciences, August 2012, Vol. 37, No. 8: 333-41. doi: 10.1016/j.tibs.2012.05.001 PMID: 22705166
    • (2012) Trends in Biochemical Sciences , vol.37 , Issue.8 , pp. 333-341
    • Weatheritt, R.J.1    Gibson, T.J.2
  • 31
    • 84925285850 scopus 로고    scopus 로고
    • Rsp5/Nedd4 is the main ubiqui-tin ligase that targets cytosolic misfolded proteins following heat stress
    • Dec PMID: 25344756
    • Fang NN, Chan GT, Zhu M, Comyn SA, Persaud A, Deshaies RJ, et al. Rsp5/Nedd4 is the main ubiqui-tin ligase that targets cytosolic misfolded proteins following heat stress. Nature Cell Biology, 2014 Dec; 16(12):1227-37. doi: 10.1038/ncb3054 PMID: 25344756
    • (2014) Nature Cell Biology , vol.16 , Issue.12 , pp. 1227-1237
    • Fang, N.N.1    Chan, G.T.2    Zhu, M.3    Comyn, S.A.4    Persaud, A.5    Deshaies, R.J.6
  • 32
    • 0037099666 scopus 로고    scopus 로고
    • Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor
    • PMID: 12110597
    • Derbyshire D.J., et al. (2002) Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor. Embo J. 21:3863-72. PMID: 12110597
    • (2002) Embo J. , vol.21 , pp. 3863-3872
    • Derbyshire, D.J.1
  • 33
    • 84928008028 scopus 로고    scopus 로고
    • Overcome support vector machine diagnosis overfitting
    • Dec 9. PMID: 25574125
    • Han H, Jiang X. Overcome support vector machine diagnosis overfitting. Cancer Inform. 2014 Dec 9. 13:145-58. doi: 10.4137/CIN.S13875 PMID: 25574125
    • (2014) Cancer Inform. , vol.13 , pp. 145-158
    • Han, H.1    Jiang, X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.