Profile-based short linear protein motif discovery

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Haslam, Niall J ^a   Shields, Denis C ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

Mini motifs; Motif discovery; Peptide binding; Protein protein interactions; Short linear motifs; SLiMs

Indexed keywords

MINI-MOTIFS; MOTIF DISCOVERY; PEPTIDE BINDING; PROTEIN-PROTEIN INTERACTIONS; SHORT LINEAR MOTIFS; SLIMS;

AMINO ACIDS; PATTERN MATCHING;

PROTEINS;

PROTEIN;

ARTICLE; CHEMISTRY; HUMAN; METHODOLOGY; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

AMINO ACID MOTIFS; CONSERVED SEQUENCE; DATABASES, PROTEIN; HUMANS; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

MLCS; MLOWN;

EID: 84861175619     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-104     Document Type: Article

References (40)

1. Neduva V, Russell RB. Linear motifs: evolutionary interaction switches. FEBS Lett 2005, 579:3342-3345. 10.1016/j.febslet.2005.04.005, 15943979.
2. Letunic I, Doerks T, Bork P. SMART 6: recent updates and new developments. Nucleic Acids Res 2009, 37:D229-D232. 10.1093/nar/gkn808, 2686533, 18978020.
3. Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, et al. ELM-the database of eukaryotic linear motifs. Nucleic Acids Res 2012, 40:D242-251. 10.1093/nar/gkr1064, 3245074, 22110040.
4. Miller MLL, Jensen LJJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, et al. Linear motif atlas for phosphorylation-dependent signaling. Sci Signal 2008, 1:ra2. 10.1126/scisignal.1159433, 18765831.
5. Gibson TJ. Cell regulation: determined to signal discrete cooperation. Trends Biochem Sci 2009, 34:471-482. 10.1016/j.tibs.2009.06.007, 19744855.
6. Rajasekaran S, Balla S, Gradie P, Gryk MRR, Kadaveru K, Kundeti V, Maciejewski MWW, Mi T, Rubino N, Vyas J, Schiller MRR. Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res 2008,
7. Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Res 2010, 39:D261-D267. 3013696, 21062810.
8. Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol 2007, 8(11):R250. 10.1186/gb-2007-8-11-r250, 2258193, 18039369.
9. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004, 337:635-645. 10.1016/j.jmb.2004.02.002, 15019783.
10. Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, et al. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res 2010, 38:D167-180. 10.1093/nar/gkp1016, 2808914, 19920119.
11. Via A, Gould C, Gemund C, Gibson T, Citterich MH. A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinforma 2009, 10.
12. Down TA, Bergman CM, Su J, Hubbard TJ. Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput Biol 2007, 3:e7. 10.1371/journal.pcbi.0030007, 1779301, 17238282.
13. Bailey TL. Discovering novel sequence motifs with MEME. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al] 2002, Chapter 2:Unit 2.4.
14. Neduva V, Russell RB. DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res 2006, 34.
15. Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Res 2010, 1-6.
16. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37:W202-208. 10.1093/nar/gkp335, 2703892, 19458158.
17. Diella F, Haslam N, Chica C, Budd A, Michael S, Brown NP, Trave G, Gibson TJ. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 2008, 13:6580-6603.
18. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004, 14:1188-1190. 10.1101/gr.849004, 419797, 15173120.
19. Davey NE, Shields DC, Edwards RJ. Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics (Oxford, England) 2009, 25:443-450.
20. Consortium TU. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 2010, 38:D142-D148. 2808944, 19843607.
21. Fuxreiter M, Tompa P, Simon I. Local structural disorder imparts plasticity on linear motifs. Bioinformatics (Oxford, England) 2007, 23:950-956.
22. Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ. Attributes of short linear motifs. Mol Biosyst 2011, 8:268-281.
23. Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, et al. Ensembl 2009. Nucleic Acids Res 2009, 37:D690-D697. 10.1093/nar/gkn828, 2686571, 19033362.
24. Edwards RJ, Davey NE, Shields DC. SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins. PLoS One 2007, 2(10):e967. 10.1371/journal.pone.0000967, 1989135, 17912346.
25. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma 2004, 5:113.
26. Davey NE, Edwards RJ, Shields DC. The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res 2007, 35:W455-459. 10.1093/nar/gkm400, 1933137, 17576682.
27. Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics (Oxford, England) 2005, 21:3433-3434.
28. Neduva V, Russell R. Linear motifs: evolutionary interaction switches. FEBS Lett 2005, 579:3342-3345. 10.1016/j.febslet.2005.04.005, 15943979.
29. Gould CM, Diella F, Via A, Puntervoll P, Gemund C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C. Others: ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res 2010, 38:D167. 10.1093/nar/gkp1016, 2808914, 19920119.
30. Prasad TS, Kandasamy K, Pandey A. Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol 2009, 577:67-79. 10.1007/978-1-60761-232-2_6, 19718509.
31. Laskowski RA, Swindells MB. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 2011, 51:2778-2786. 10.1021/ci200227u, 21919503.
32. Fan J, Zhang Q, Tochio H, Li M, Zhang M. Structural basis of diverse sequence-dependent target recognition by the 8 kDa dynein light chain. J Mol Biol 2001, 306:97-108. 10.1006/jmbi.2000.4374, 11178896.
33. Benison G, Karplus PA, Barbar E. The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8. J Mol Biol 2008, 384:954-966. 10.1016/j.jmb.2008.09.083, 18948118.
34. Williams JC, Roulhac PL, Roy AG, Vallee RB, Fitzgerald MC, Hendrickson WA. Structural and thermodynamic characterization of a cytoplasmic dynein light chain-intermediate chain complex. Proc Natl Acad Sci U S A 2007, 104:10028-10033. 10.1073/pnas.0703614104, 1885999, 17551010.
35. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
36. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539.
37. Doǧruel M, Down T, Hubbard TJ. NestedMICA as an ab initio protein motif discovery tool. BMC Bioinforma 2008, 9:19.
38. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011, 39:W29-37. 10.1093/nar/gkr367, 3125773, 21593126.
39. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz H-R, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A. The Pfam protein families database. Nucleic Acids Res 2008, 36:D281-D288. 10.1093/nar/gkn226, 2238907, 18039703.
40. Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMSearch 2.0 : biological context for short linear motifs in proteins. Nucleic Acids Res 2011, Webserver 1-5.