ProteinParser-A community based tool for the generation of a detailed protein consensus and FASTA output

Computer Methods and Programs in Biomedicine

Volumn 85, Issue 1, 2007, Pages 69-76

  Ryan, Barry J ^a   Barrett, Ronan ^b  

^a DUBLIN CITY UNIVERSITY   (Ireland)

^b DUBLIN CITY UNIVERSITY   (Ireland)

Author keywords

Amino acid frequency counting; Consensus concept; Protein alignment; Protein stabilisation

Indexed keywords

AMINO ACIDS; BACTERIA; COMPUTER AIDED SOFTWARE ENGINEERING; JAVA PROGRAMMING LANGUAGE; MATHEMATICAL MODELS; MUTAGENESIS;

AMINO ACID FREQUENCY COUNTING; CONSENSUS CONCEPT; PROTEIN ALIGNMENT; PROTEIN STABILIZATION;

PROTEINS;

AMINO ACID; BACTERIAL ENZYME; BETA LACTAMASE; PHYTASE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; CONSENSUS; INFORMATION PROCESSING; INFORMATION SYSTEM; MUTAGENESIS; PROTEIN ANALYSIS; PROTEIN MICROARRAY; PROTEIN STABILITY; PROTEINPARSER;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 37849187275     PISSN: 01692607     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cmpb.2006.09.015     Document Type: Article

References (24)

1. Levitt M., and Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 5913-5920
2. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., and Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucl. Acids Res. 31 (2003) 3497-3500
3. Notredame C., Higgins D., and Heringa J. T-Coffee: a novel method for multiple sequence alignments. J. Mol. Biol. 302 (2000) 205-217
4. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucl. Acids Res. 16 (1988) 10881-10890
5. Lassmann T., and Sonnhammer E.L.L. Quality assessment of multiple alignment programs. FEBS Lett. 529 (2002) 126-130
6. Lehmann M., and Wyss M. Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr. Opin. Biotechnol. 12 (2001) 371-375
7. Miyazaki J., Nakaya S., Suzuki T., Tamakoshi M., Oshima T., and Yamagishi A. Ancestral residues stabilising 3-isopropylmalate dehydrogenase of an extreme thermopile: experimental evidence supporting the thermophilic common ancestor hypothesis. J. Biochem. 129 (2001) 777-782
8. Lehmann M., Loch C., Middendorf A., Studer D., Lassen S.F., Pasamontes L., van Loon A.P.G.M., and Wyss M. The consensus concept for thermostability engineering of proteins: further proof of concept. Protein Eng. 15 (2002) 403-411
9. Flores H., and Ellington A.D. A modified consensus approach to mutagenesis inverts the co-factor specificity of Bacillus stearothermophilus lactate dehydrogenase. Protein Eng. Des. Sel. 18 (2005) 369-377
10. van den Burg B., and Eijsink V.G.H. Selection for increased protein stability. Curr. Opin. Biotechnol. 13 (2002) 333-337
11. Lehmann M., Pasamontes L., Lassen S.F., and Wyss M. The consensus concept for thermostability engineering of proteins. Biochim. Biophys. Acta 1543 (2000) 408-415
12. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
13. Lethbridge T.C., and Laganiere R. Object-OrientedSoftware Engineering: Practical Software Development Using UML and Java. second ed. (2004), McGraw-Hill, New York
14. Amin N., Liu A.D., Ramer S., Aehle W., Meijer D., Metin M., Wong S., Gualfetti P., and Schellenberger V. Construction of stabilised proteins by combinatorial consensus mutagenesis. Protein Eng. Des. Sel. 17 (2004) 787-793
15. Schellenberger, Personal Communication, 16 January 2006.
16. Magliery T.J., and Regan L. Beyond consensus: statistical free energies reveal hidden interactions in the design of TPR Motif. J. Mol. Biol. 343 (2004) 731-745
17. Pantoliano M.W., Whitlow M., Wood J.F., Dodd S.W., Hardman K.D., Rollence M.L., and Bryan P.N. Large increases in general stability for Subtilisin BPN′ through incremental changes in free energy of unfolding. Biochemistry 28 (1989) 7205-7213
18. Eijsink V.G.H., Bjork A., Gaseidnes S., Sirevag R., Synstad B., van der Berg B., and Vriend G. Rational design of enzyme stability. J. Biotechnol. 113 (2004) 105-120
19. Hall B.G. Simple and accurate estimation of ancestral protein sequences. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 5431-5436
20. Chang B.S.W., Jönsson K., Kazmi M.A., Donoghue M.J., and Sakmar T.P. Recreating a functional ancestral archosaur visual pigment. Mol. Biol. Evol. 19 (2002) 1483-1489
21. Parry-Smith D.J., Payne A.W.R., Michie A.D., and Attwood T.K. CINEMA-a novel Colour INteractive Editor for Multiple Alignments. Gene 211 (1997) GC45-GC56
22. Gilis D., and Rooman M. PoPMuSiC: an algorithm for predicting protein mutant stability changes. Application to prion proteins. Protein Eng. 13 (2000) 849-856
23. Nicholas K.B., Nicholas Jr. H.B., and Deerfield D.W. GeneDoc: analysis and visualization of genetic variation. EMBNEW News 4 (1997) 14
24. Damblon C., Raquet X., Lian L.Y., Lamotte-Brasseur J., Fonze E., Charlier P., Roberts G.C., and Frere J.M. The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 1747-1752