CaSPredictor: A new computer-based tool for caspase substrate prediction

Bioinformatics

Volumn 21, Issue SUPPL. 1, 2005, Pages

  Garay Malpartida, H M ^a   Occhiucci, J M ^a   Alves, J ^a   Belizario J E ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; ASPARTIC ACID; CASPASE; GLUTAMIC ACID; GLUTAMINE; PROLINE; SERINE; THREONINE;

ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CELLULAR DISTRIBUTION; COMPUTER PROGRAM; CORRELATION ANALYSIS; ENZYME SUBSTRATE; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; RECEIVER OPERATING CHARACTERISTIC; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE;

CASPASES; CLEAVAGE SITES; COMPUTER BASED TOOLS; DATA FILES; DATA SETS; FOUR AMINO ACIDS; IN-VITRO; IN-VIVO; INDIVIDUAL PROTEINS; NATURAL SUBSTRATES; PRIMARY SEQUENCES; PROTEOLYTIC CLEAVAGE; STRUCTURAL RELATIONSHIP; SUBSTRATE RECOGNITION; SUBSTRATE SELECTION;

AMINO ACIDS; FORECASTING; INTELLIGENT SYSTEMS; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; PROTEINS; SITE SELECTION;

SUBSTRATES;

EID: 29144473665     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1034     Document Type: Article

References (24)

1. Belizário,J.E., Lorite,M.J. and Tisdale,M.J. (2001) Cleavage of caspases-1,-3,-6, -8 and -9 substrates by proteases in skeletal muscle from mice undergoing cancer cachexia. Br. J. Cancer, 84, 1135-1140.
2. Boatright,K.M., Renatus,M., Scott,F.L., Sperandio,S., Shin,H., Pedersen,I.M., Ricci,J.E., Edris,W.A., Sutherlin,D.P., Green,D.R. and Salvesen,G.S. (2003) A unified model for apical caspase activation. Mol. Cell, 11, 529-541.
3. Chai,J., Shiozaki,E., Srinivasula,S.M., Wu,Q., Dataa,P., Alnemri,E.S. and Shi,Y. (2001) Crystal structure of a procaspase-7 zymogen: mechanisms of activation and substrate binding. Cell, 107, 399-407
4. Cohen,G.M. (1997) Caspases: The executioner of apoptosis. Biochem. J., 326, 1-16.
5. Doctor,K.S, Reed,J.C, Godzik,A. and Bourne,P.E. (2003) The apoptosis database. Cell Death Differ., 10, 621-633.
6. Du,J., Wang,X., Miereles,C., Bailey,J.L., Debigare,R., Zheng,B., Price,S.R. and Mitch,W.E. (2004) Activation of caspase-3 is an initial step triggering accelerated muscle proteolysis in catabolic conditions. J. Clin. Invest., 113, 115-123.
7. Earnshaw,W.C., Martins,L.M. and Kaufmann,S.H. (1999) Mammalian caspases: structure, activation, substrates, and functions during apoptosis. Annu. Rev. Biochem., 68, 383-424.
8. Fischer,U., Jänicke,R.U. and Schulze-Osthoff,K. (2003) Many cuts to ruin: A comprehensive update of caspase substrates. Cell Death Differ., 10, 76-100.
9. Garcia-Calvo,M. (1997)A combinatorial approach defines specificities of members of the caspase family and granzyme B. J. Biol. Chem., 272, 17907-17911.
10. Hanley,J.A. and McNeil,B.J. (1982) The meaning and use of the area under the receiver operating characteristic (ROC) curve. Radiology, 143, 29-36.
11. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
12. Lamkanfi,M., Declercq,W., Kalai,M., Saelens,X. and Vandenabeele,P. (2002) Alice in caspase land. A phylogenetic analysis of caspases from worm to man. Cell Death Differ., 9, 358-361.
13. Lohmüller,T., Wenzler,D., Hagemann,S., Kieb,W., Peters,C., Dandekar,T. and Reinheckel,T. (2003) Toward computer-based cleavage site prediction of cysteine endopeptidades. Biol. Chem., 384, 899-909.
14. Rechsteiner,M. and Rogers,S.W. (1996) PEST sequences and regulation by proteolysis. Trends Biochem Sci., 21, 267-271.
15. Riedl,S.J., Prior,P.F., Renatus,M., Kairies,N., Krapp,S., Huber,R., Salveseen,G. and Bode,W. (2001) Structural basis for the activation of human procaspase-7. Proc. Natl Acad. Sci. USA, 98, 14790-14795.
16. Rogers,S., Wells,R. and Rechsteiner,M. (1986) Amino acid sequences common to rapidly degraded proteins: The PEST hypothesis. Science, 234, 364-368.
17. Schwerk,C. and Schulze-Osthoff,K. (2003) Non-apoptotic functions of caspases in cellular proliferation and differentiation. Biochem. Pharmacol., 66, 1453-1458.
18. Talanian,R.V., Quinlan,C., Trautz,S., Hackett,M.C., Mankovich,J.A., Banach,D., Ghayur,T., Brady,K.D. and Wong,W.W. (1997) Substrate specificity of caspase family proteases. J. Biol. Chem., 272, 9677-9682.
19. Thomson,R., Hodgman,T.C., Yang,Z.R. and Doyle,A.K. (2004) Characterizing proteolytic cleavage site activity using bio-basis function neural networks. Bioinformatics, 19, 1741-1747.
20. Thornberry,N.A., Rano,T.A., Peterson,E.P., Raper,D.M., Timkey,T., Garcia-Calvo,M., et al. (1997) A combinatorial approach defines specificities of members of the caspase family and granzyme B. J. Biol. Chem., 272, 17907-17911.
21. Tompa,P. (2002) Intrinsically unstructured proteins. Trends Biochem. Sci., 27, 527-533.
22. Tompa,P., Buzder-Lantos,P., Tantos,A., Farkas,A., Szilágyi,A., Bánóczi,Z., Hudecz,F. and Friedrich,P. (2004) On the sequential determinants of calpain cleavage. J. Biol. Chem., 279, 20775-20785.
23. Wright,P.E. and Dyson,H.J. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol., 293, 321-331.
24. Yang,Z.R. and Chou,K.C. (1997) Predicting the linkage sites in glycoproteins using bio-basis function neural network. Bioinformatics, 20(6), 903-908.