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Cited by 647

The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.

Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels

Russell, Robert B., Barton, Geoffrey J.·1992·Proteins: Structure, Function, and Bioinformatics
DOI 10.1002/prot.340140216
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Abstract

An algorithm is presented for the accurate and rapid generation of multiple protein sequence alignments from tertiary structure comparisons. A preliminary multiple sequence alignment is performed using sequence information, which then determines an initial superposition of the structures. A structure comparison algorithm is applied to all pairs of proteins in the superimposed set and a similarity tree calculated. Multiple sequence alignments are then generated by following the tree from the branches to the root. At each branchpoint of the tree, a structure‐based sequence alignment and coordinate transformations are output, with the multiple alignment of all structures output at the root The algorithm encoded in STAMP (Structural Alignment of Multiple Proteins) is shown to give alignments in good agreement with published structural accounts within the dehydrogenase fold domains, globins, and serine proteinases. In order to reduce the need for visual verification, two similarity indices are introduced to determine the quality of each generated structural alignment. S c quantifies the global structural similarity between pairs or groups of proteins, whereas Pij′ provides a normalized measure of the confidence in the alignment of each residue. STAMP alignments have the quality of each alignment characterized by Sc and Pij′ values and thus provide a reproducible resource for studies of residue conservation within structural motifs. © 1992 Wiley‐Liss, Inc.

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Research works printed but not linked: 20

  1. 10.1073/pnas.75.5.2180 · doi:10.1073/pnas.75.5.2180
  2. 10.1016/S0263-7855(98)80002-7 · doi:10.1016/s0263-7855(98)80002-7
  3. Adman E. T., 1984, Metalloproteins: Metal Proteins with Redox Rules, 1
  4. 10.1107/S0567739472001627 · doi:10.1107/s0567739472001627
  5. 10.1107/S0567739476000016 · doi:10.1107/s0567739476000016
  6. 10.1101/SQB.1972.036.01.025 · doi:10.1101/sqb.1972.036.01.025
  7. 10.1142/9789814360401 · doi:10.1142/9789814360401
  8. 10.1016/S0022-2836(83)80160-0 · doi:10.1016/s0022-2836(83)80160-0
  9. 10.1038/295535a0 · doi:10.1038/295535a0
  10. 10.1016/0022-2836(73)90377-X · doi:10.1016/0022-2836(73)90377-x
  11. 10.1016/0022-2836(78)90071-2 · doi:10.1016/0022-2836(78)90071-2
  12. 10.1021/bi00338a005 · doi:10.1021/bi00338a005
  13. 10.1107/S010876818500177X · doi:10.1107/s010876818500177x
  14. 10.1016/0022-2836(83)90077-3 · doi:10.1016/0022-2836(83)90077-3
  15. 10.1021/bi00321a045 · DOI
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  17. 10.1016/0022-2836(79)90200-6 · doi:10.1016/0022-2836(79)90200-6
  18. Grau U. M., 1980, The 2.7 Å x‐ray structure of pig LDH a very close representation of the active ternary complex of lactate dehydrogenase, American Crystallographic Association, Abstracts Papers, 8, 39
  19. Branden C. I., 1986, Interdomain motion in liver alcohol dehydrogenase. structural and energetic analysis of the hinge bending mode, J. Biol. Chem., 261, 15273, 10.1016/S0021-9258(18)66863-2 · doi:10.1016/s0021-9258(18)66863-2
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Metadata

Authors
Russell, R. B., & Barton, G. J.
Venue
Proteins: Structure, Function, and Bioinformatics
Publisher
Wiley
Published
1992-10
Volume
14
Issue
2
Pages
309-323
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
DOI
10.1002/prot.340140216
OpenAlex
W2084367350
Cited by
647
References
43
FWCI
3.44
Type
journal article
Language
en
Open access
closed
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor, 4142 d)

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