Twilight zone of protein sequence alignments
10.1093/protein/12.2.85
Crossref journal-article
Oxford University Press (OUP)
Protein Engineering, Design and Selection (286)
Bibliography

Rost, B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, Design and Selection, 12(2), 85–94.

Authors 1
  1. Burkhard Rost (first)
References 69 Referenced 1,424
  1. Abagyan,R.A. and Batalov,S. (1997) J. Mol. Biol., 273, 355–368. (10.1006/jmbi.1997.1287)
  2. Alexandrov,N.N. and Soloveyev,V.V. (1998) In Altman,R.B., Dunker,A.K., Hunter,L. and Klein,T.E. (eds) HICCS' 98: Pacific Symposium on Biocomputing' 98. Maui, Hawaii, USA, pp. 463–472.
  3. Alexandrov,N.N., Takahashi,K. and Go,N. (1992) J. Mol. Biol., 225, 5–9. (10.1016/0022-2836(92)91021-G)
  4. Altschul,S., Madden,T., Shaffer,A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (1997) Nucleic Acids Res., 25, 3389–3402. (10.1093/nar/25.17.3389)
  5. Altschul,S.F. and Gish,W. (1996) Methods Enzymol., 266, 460–480. (10.1016/S0076-6879(96)66029-7)
  6. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) J. Mol. Biol., 215, 403–410. (10.1016/S0022-2836(05)80360-2)
  7. Bairoch,A. and Apweiler,R. (1997) Nucleic Acids Res., 25, 31–36. (10.1093/nar/25.1.31)
  8. Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F., Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) J. Mol. Biol., 112, 535–542. (10.1016/S0022-2836(77)80200-3)
  9. Brenner,S.E., Chothia,C. and Hubbard,T.J.P. (1998) Proc. Natl Acad. Sci. USA, 95, 6073–6078. (10.1073/pnas.95.11.6073)
  10. Brenner,S.E., Chothia,C., Hubbard,T.J.P. and Murzin,A.G. (1996) Methods Enzymol., 266, 635–643. (10.1016/S0076-6879(96)66039-X)
  11. Bryant,S.H. and Altschul,S.F. (1995) Curr. Opin. Struct. Biol., 5, 236–244. (10.1016/0959-440X(95)80082-4)
  12. Casari,G., Sander,C. and Valencia,A. (1995) Nature Struct. Biol., 2, 171–178. (10.1038/nsb0295-171)
  13. Cerpa,R., Cohen,F.E. and Kuntz,I.D. (1996) Folding Des., 1, 91–101. (10.1016/S1359-0278(96)00018-1)
  14. Chothia,C. (1992) Nature, 357, 543–544. (10.1038/357543a0)
  15. Chothia,C. and Lesk,A.M. (1986) EMBO J., 5, 823–826.
  16. Chung,S.Y. and Subbiah,S. (1996) Structure, 4, 1123–1127. (10.1016/S0969-2126(96)00119-0)
  17. Cohen,B.I., Presnell,S.R. and Cohen,F.E. (1993) Protein Sci., 2, 2134–2145. (10.1002/pro.5560021213)
  18. Crippen,G.M. and Maiorov,V.N. (1995) J. Mol. Biol., 252, 144–151. (10.1006/jmbi.1995.0481)
  19. Doolittle,R.F. (1979) In Neurath,H. and Hill,R.L. (eds) Protein Evolution. Academic Press, New York, pp. 1–118. (10.1016/B978-0-12-516304-0.50006-4)
  20. Doolittle,R.F. (1981) Science, 214, 149–159. (10.1126/science.7280687)
  21. Doolittle,R.F. (1986) Of URFs and ORFs: a primer on how to analyze derived amino acid sequences. University Science Books, Mill Valley, CA, USA.
  22. Doolittle,R.F. (1994) TIBS, 19, 15–18. (10.1016/0968-0004(94)90167-8)
  23. Fischer,D. and Eisenberg,D. (1996) Protein Sci., 5, 947–955. (10.1002/pro.5560050516)
  24. Fischer,D., Rice,D.W., Bowie,J.U. and Eisenberg,D. (1996) FASEB J., 10, 126–136.
  25. Gerstein,M. and Levitt,M. (1996) In States,D., Agarwal,P., Gaasterland,T., Hunter,L. and Smith,R.F. (eds) Fourth International Conference on Intelligent Systems for Molecular Biology, AAAI, St Louis, MO, USA, pp. 59–67.
  26. Gotoh,O. (1996) J. Mol. Biol., 264, 823–838. (10.1006/jmbi.1996.0679)
  27. Gribskov,M., McLachlan,M. and Eisenberg,D. (1987) Proc. Natl Acad. Sci. USA, 84, 4355–5358. (10.1073/pnas.84.13.4355)
  28. Hobohm,U., Scharf,M., Schneider,R. and Sander,C. (1992) Protein Sci., 1, 409–417. (10.1002/pro.5560010313)
  29. Holm,L., Ouzounis,C., Sander,C., Tuparev,G. and Vriend,G. (1993) Protein Sci., 1, 1691–1698. (10.1002/pro.5560011217)
  30. Holm,L. and Sander,C. (1996) Nucleic Acids Res., 25, 231–234. (10.1093/nar/25.1.231)
  31. Holm,L. and Sander,C. (1997) Proteins, 28, 72–82. (10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L)
  32. Holmes,K.C., Sander,C. and Valencia,A. (1993) TICB, 3, 53–59. (10.1016/0962-8924(93)90161-S)
  33. Hubbard,T.J.P., Murzin,A.G., Brenner,S.E. and Chothia,C. (1997) Nucleic Acids Res., 25, 236–239. (10.1093/nar/25.1.236)
  34. Kabsch,W. and Sander,C. (1984) Proc. Natl Acad. Sci. USA, 81, 1075–1078. (10.1073/pnas.81.4.1075)
  35. Lemer,C.M.-R., Rooman,M.J. and Wodak,S.J. (1995) Proteins, 23, 337–355. (10.1002/prot.340230308)
  36. Luo,Y., Lai,L., Xu,X. and Tang,Y. (1993) Protein Engng, 6, 373–376. (10.1093/protein/6.4.373)
  37. Maiorov,V.N. and Crippen,G.M. (1995) Proteins, 22, 273–283. (10.1002/prot.340220308)
  38. Minor,D.L.J. and Kim,P.S. (1996) Nature, 380, 730–734. (10.1038/380730a0)
  39. Muñoz,V. and Serrano,L. (1996) Folding Des., 1, R71–R77. (10.1016/S1359-0278(96)00036-3)
  40. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) J. Mol. Biol., 247, 536–540.
  41. Neuwald,A.F., Liu,J.S., Lipman,D.J. and Lawrence,C.E. (1997) Nucleic Acids Res., 25, 1665–1677. (10.1093/nar/25.9.1665)
  42. Nielsen,H., Engelbrecht,J., von Heijne,G. and Brunak,S. (1996) Proteins, 24, 165–177. (10.1002/(SICI)1097-0134(199602)24:2<165::AID-PROT4>3.0.CO;2-I)
  43. Orengo,C. (1994) Curr. Opin. Struct. Biol., 4, 429–440. (10.1016/S0959-440X(94)90113-9)
  44. Orengo,C.A. and Taylor,W.R. (1996) Meth. Enzymol., 266, 617–635. (10.1016/S0076-6879(96)66038-8)
  45. Orengo,C.A., Flores,T.P., Taylor,W.R. and Thornton,J.M. (1993) Protein Engng, 6, 485–500. (10.1093/protein/6.5.485)
  46. Orengo,C.A., Michie,A.D., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) Structures, 5, 1093–1108. (10.1016/S0969-2126(97)00260-8)
  47. Park,J., Teichmann,S.A., Hubbard,T. and Chothia,C. (1997) J. Mol. Biol., 273, 349–354. (10.1006/jmbi.1997.1288)
  48. Pascarella,S. and Argos,P. (1992) Protein Engng, 5, 121–137. (10.1093/protein/5.2.121)
  49. Pearson,W.R. (1996) Methods Enzymol., 266, 227–258. (10.1016/S0076-6879(96)66017-0)
  50. Rost,B. (1996) Methods Enzymol., 266, 525–539. (10.1016/S0076-6879(96)66033-9)
  51. Rost,B. (1997) Folding Des., 2, S19–S24. (10.1016/S1359-0278(97)00059-X)
  52. Rost,B. and O'Donoghue,S.I. (1997) CABIOS, 13, 345–356. (10.1093/bioinformatics/13.4.345)
  53. Rost,B. and Sander,C. (1996) Annu. Rev. Biophys. Biomol. Struct., 25, 113–136. (10.1146/annurev.bb.25.060196.000553)
  54. Rost,B., Schneider,R. and Sander,C. (1997) J. Mol. Biol., 270, 471–480. (10.1006/jmbi.1997.1101)
  55. Rost,B. (1997) WWW document (http://www.embl-heidelberg.de/predictprotein). EMBL.
  56. Rost,B. (1998) WWW document (http://www.embl-heidelberg.de/~rost/Papers/Dfig/98twilight/app.html). EMBL.
  57. Russell,R.B., Copley,R.R. and Barton,G.J. (1996) J. Mol. Biol., 259, 349–365. (10.1006/jmbi.1996.0325)
  58. Sander,C. and Schneider,R. (1991) Proteins, 9, 56–68. (10.1002/prot.340090107)
  59. Schneider,R. (1994) PhD, University of Heidelberg.
  60. Schneider,R., de Daruvar,A. and Sander,C. (1997) Nucleic Acids Res., 25, 226–230. (10.1093/nar/25.1.226)
  61. Sippl,M.J. (1995) Curr. Opin. Struct. Biol., 5, 229–235. (10.1016/0959-440X(95)80081-6)
  62. Sippl,M.J. and Floeckner,H. (1996) Structure, 4, 15–19. (10.1016/S0969-2126(96)00005-6)
  63. Smith,T.F. and Waterman,M.S. (1981) J. Mol. Biol., 147, 195–197. (10.1016/0022-2836(81)90087-5)
  64. Valencia,A., Kjeldgaard,M., Pai,E.F. and Sander,C. (1991) Proc. Natl Acad. Sci. USA, 88, 5443–5447. (10.1073/pnas.88.12.5443)
  65. Vogt,G., Etzold,T. and Argos,P. (1995) J. Mol. Biol., 249, 816–831. (10.1006/jmbi.1995.0340)
  66. Wodak,S.J. and Rooman,M.J. (1993) Curr. Opin. Struct. Biol., 3, 247–259. (10.1016/S0959-440X(05)80160-5)
  67. Zu-Kang,F. and Sippl,M.J. (1996) Folding Des., 1, 123–132. (10.1016/S1359-0278(96)00021-1)
  68. Zuckerkandl,E. (1976) J. Mol. Evol., 7, 269–311. (10.1007/BF01743626)
  69. Zuckerkandl,E. and Pauling,L. (1965) In Bryson,V. and Vogel,H.J. (eds) Evolutionary Divergence and Convergence in Proteins. Academic Press, New York; London, pp. 97–166. (10.1016/B978-1-4832-2734-4.50017-6)
Dates
Type When
Created 23 years, 1 month ago (July 26, 2002, 2:38 p.m.)
Deposited 5 years, 6 months ago (March 3, 2020, 10:51 p.m.)
Indexed 1 hour, 5 minutes ago (Sept. 4, 2025, 4:53 a.m.)
Issued 26 years, 7 months ago (Feb. 1, 1999)
Published 26 years, 7 months ago (Feb. 1, 1999)
Published Online 26 years, 7 months ago (Feb. 1, 1999)
Published Print 26 years, 7 months ago (Feb. 1, 1999)
Funders 0

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@article{Rost_1999, title={Twilight zone of protein sequence alignments}, volume={12}, ISSN={1741-0126}, url={http://dx.doi.org/10.1093/protein/12.2.85}, DOI={10.1093/protein/12.2.85}, number={2}, journal={Protein Engineering, Design and Selection}, publisher={Oxford University Press (OUP)}, author={Rost, Burkhard}, year={1999}, month=feb, pages={85–94} }