MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences

Nucleic Acids Research

Volumn 44, Issue W1, 2016, Pages W488-W493

  Malhis, Nawar ^a   Jacobson, Matthew ^a   Gsponer, Jörg ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

INTRINSICALLY DISORDERED PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PREDICTION; MACHINE LEARNING; MOLECULAR RECOGNITION; PROPENSITY SCORE; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT;

EID: 85024097785     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/NAR/GKW409     Document Type: Article

References (24)

1. Babu,M., Lee,R.V.D., DeGroot,N.S. and Gsponer,J. (2011) Intrinsically disordered proteins: regulation and disease. Curr. Opin. Struct. Biol., 21, 1-9.
2. Weatheritt,R.J. and Gibson,T.J. (2012) Linear motifs: lost in (pre)translation. Trends Biochem. Sci., 37, 333-341.
3. Mohan,A., Oldfield,C.J., Radivojac,P., Vacic,V., Cortese,M.S., Dunker,A.K. and Uversky,V.N. (2006) Analysis of molecular recognition features (MoRFs). J. Mol. Biol., 362, 1043-1059.
4. Cumberworth,A., Lamour,G., Babu,M.M. and Gsponer,J. (2013) Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes. Biochem. J., 454, 361-369.
5. Oldfield,C.J., Cheng,Y., Cortese,M.S., Romero,P., Uversky,V.N. and Dunker,A.K. (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry, 44, 12454-12470.
6. Vacic,V., Oldfield,C.J., Mohan,A., Radivojac,P., Cortese,M.S., Uversky,V.N. and Dunker,A.K. (2007) Characterization of molecular recognition features, MoRFs, and their binding partners. J. Proteome Res., 6, 2351-2366.
7. Cheng,Y., Oldfield,C.J., Meng,J., Romero,P., Uversky,V.N. and Dunker,A.K. (2007) Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry, 46, 13468-13477.
8. Yan,J., Dunker,A.K., Uversky,V. and Kurgan,L. (2016) Molecular recognition features (MoRFs) in three domains of life. Mol. BioSyst., 12, 697-710.
9. Mészáros,B., Simon,I. and Dosztányi,Z. (2009) Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol., 5, e1000376.
10. Disfani,F.M., Hsu,W.L., Mizianty,M.J., Oldfield,C.J., Xue,B., Dunker,A.K. et al. (2012) MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics, 28, i75-i83.
11. Fang,C., Noguchi,T., Tominaga,D. and Yamana,H. (2013) MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation. BMC Bioinformatics, 14, 300.
12. Jones,D.T. and Cozzetto,D. (2015) DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics, 31, 857-863.
13. Malhis,N. and Gsponer,J. (2015) Computational identification of MoRFs in protein sequences. Bioinformatics, 31, 1738-1744.
14. Malhis,N., Wong,T.C.E., Nassar,R. and Gsponer,J. (2015) Computational identification of MoRFs in protein sequences using hierarchical application of bayes rule. PLoS One, 10, doi:10.1371/journal.pone.0141603.
15. Oldfield,C.J., Cheng,Y., Cortese,M.S., Romero,P., Uversky,V.N. and Dunker,A.K. (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry, 44,12454-12470.
16. Cheng,Y., Oldfield,C.J., Meng,J., Romero,P., Uversky,V.N. and Dunker,A.K. (2007) Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry, 46, 13468-13477.
17. Xue,B., Dunker,A.K. and Uversky,V.N. (2010) Retro-MoRFs: identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction. Int. J. Mol. Sci., 11, 3725-3747.
18. Peng,Z. and Kurgan,L. (2015) High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder. Nucleic Acids Res., 43, e121.
19. Walsh,I., Martin,A.J., Di Domenico,T. and Tosatto,S.C. (2012) ESpritz: accurate and fast prediction of protein disorder. Bioinformatics, 28, 503-509.
20. Mészáros,B., Tompa,P., Simon,I. and Dosztányi,Z. (2007) Molecular Principles of the Interactions of Disordered Proteins. JMB, 372, 549-561.
21. Trudeau,T., Nassar,R., Cumberworth,A., Wong,E.T.C., Woollard,G. and Gsponer,J. (2013) Structure and intrinsic disorder in protein autoinhibition. Structure, 21, 332-341.
22. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res., 25, 3389-3402.
23. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
24. Sigalov,A., Aivazian,D. and Stern,L. (2004) Homooligomerization of the cytoplasmic domain of the T cell receptor zeta chain and of other proteins containing the immunoreceptor tyrosine-based activation motif. Biochemistry, 43, 2049-2061.