DOI: 10.1093/protein/gzj005. Variable gap penalty for protein sequence

Variable gap penalty for protein sequence–structure alignment

10.1093/protein/gzj005

Crossref journal-article

Oxford University Press (OUP)

Protein Engineering, Design and Selection (286)

Bibliography

Madhusudhan, M. S., Marti-Renom, M. A., Sanchez, R., & Sali, A. (2006). Variable gap penalty for protein sequenceâstructure alignment. Protein Engineering, Design and Selection, 19(3), 129â133.

Authors 4

M.S. Madhusudhan (first)
Marc A. Marti-Renom (additional)
Roberto Sanchez (additional)
Andrej Sali (additional)

References 28 Referenced 54

Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389–3402. (10.1093/nar/25.17.3389)
Bairoch,A., et al. (2005) Nucleic Acids Res., 33, D154–D159. (10.1093/nar/gki070)
Barton,G.J. and Sternberg,M.J. (1987) Protein Eng., 1, 89–94. (10.1093/protein/1.2.89)
Berman,H.M., et al. (2002) Acta Crystallogr., D58, 899–907. (10.1107/S0907444902003451)
Dayhoff,M., Schwartz,R. and Orcutt,B.C. (1978) in Daytoff,M. et al. (eds), Atlas of Protein Sequence and Sructure, National Biomedical Research Foundation, Washington, DC.
Dewey,T.G. (2001) J. Comput. Biol., 8, 177–190. (10.1089/106652701300312931)
Durbin,R., Eddy,S.R., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis: Probilistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge. (10.1017/CBO9780511790492)
Edgar,R.C. and Sjolander,K. (2004) Bioinformatics, 20, 1301–1308. (10.1093/bioinformatics/bth090)
Goonesekere,N.C. and Lee,B. (2004) Nucleic Acids Res., 32, 2838–2843. (10.1093/nar/gkh610)
Henikoff,S. and Henikoff,J.G. (2000) Adv. Protein Chem., 54, 73–97. (10.1016/S0065-3233(00)54003-0)
Lesk,A.M., Levitt,M. and Chothia,C. (1986) Protein Eng., 1, 77–78. (10.1093/protein/1.1.77)
Madhusudhan,M.S., Marti-Renom,M.A., Eswar,N., John,B., Pieper,U., Karchin,R., Shen,M.-Y. and Sali,A. (2005) in Walker,J.M. (ed.), The Proteomics Protocols Handbook, Humana Press Inc., Totowa, NJ.
Marti-Renom,M.A., Stuart,A.C., Fiser,A., Sanchez,R., Melo,F. and Sali,A. (2000) Annu. Rev. Biophys. Biomol. Struct., 29, 291–325. (10.1146/annurev.biophys.29.1.291)
Marti-Renom,M.A., Ilyin,V.A. and Sali,A. (2001) Bioinformatics, 17, 746–747. (10.1093/bioinformatics/17.8.746)
Marti-Renom,M.A., Madhusudhan,M.S., Fiser,A., Rost,B. and Sali,A. (2002) Structure (Camb.), 10, 435–440. (10.1016/S0969-2126(02)00731-1)
Marti-Renom,M.A., Madhusudhan,M.S. and Sali,A. (2004) Protein Sci., 13, 1071–1087. (10.1110/ps.03379804)
Mott,R. (1999) Bioinformatics, 15, 455–462. (10.1093/bioinformatics/15.6.455)
Moult,J. (2005) Curr. Opin. Struct. Biol., 15, 285–289. (10.1016/j.sbi.2005.05.011)
Needleman,S.B. and Wunsch,C.D. (1970) J. Mol. Biol., 48, 443–453. (10.1016/0022-2836(70)90057-4)
Pieper,U., et al. (2006) Nucleic Acids Res., 34, D291–D295. (10.1093/nar/gkj059)
Qian,B. and Goldstein,R.A. (2001) Proteins, 45, 102–104. (10.1002/prot.1129)
Rees,D. (1987) Foundation of Statistics, Chapman Hall, New York, NY.
Sali,A. and Blundell,T.L. (1993) J. Mol. Biol., 234, 779–815. (10.1006/jmbi.1993.1626)
Sali,A. and Overington,J.P. (1994) Protein Sci., 3, 1582–1596. (10.1002/pro.5560030923)
Sellers,P.H. (1974) SIAM J. Appl. Math., 26, 787–793. (10.1137/0126070)
Shi,J., Blundell,T.L. and Mizuguchi,K. (2001) J. Mol. Biol., 310, 243–257. (10.1006/jmbi.2001.4762)
Smith,T.F. and Waterman,M.S. (1981) J. Mol. Biol., 147, 195–197. (10.1016/0022-2836(81)90087-5)
Yona,G. and Levitt,M. (2002) J. Mol. Biol., 315, 1257–1275. (10.1006/jmbi.2001.5293)

Dates

Type	When
Created	19 years, 7 months ago (Jan. 19, 2006, 8:13 p.m.)
Deposited	7 years, 10 months ago (Oct. 13, 2017, 6:54 a.m.)
Indexed	1 year, 1 month ago (July 21, 2024, 1:51 a.m.)
Issued	19 years, 7 months ago (Jan. 19, 2006)
Published	19 years, 7 months ago (Jan. 19, 2006)
Published Online	19 years, 7 months ago (Jan. 19, 2006)
Published Print	19 years, 6 months ago (March 1, 2006)

Funders 0

None

BibTeX

@article{Madhusudhan_2006, title={Variable gap penalty for protein sequence–structure alignment}, volume={19}, ISSN={1741-0126}, url={http://dx.doi.org/10.1093/protein/gzj005}, DOI={10.1093/protein/gzj005}, number={3}, journal={Protein Engineering, Design and Selection}, publisher={Oxford University Press (OUP)}, author={Madhusudhan, M.S. and Marti-Renom, Marc A. and Sanchez, Roberto and Sali, Andrej}, year={2006}, month=jan, pages={129–133} }

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