The structural alignment between two proteins: Is there a unique answer?

Protein Science

Volumn 5, Issue 7, 1996, Pages 1325-1338

  Godzik, Adam ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

protein similarity; protein structural alignment

Indexed keywords

AZURIN; BINDING PROTEIN; CHEMOTACTIC PEPTIDE; COPPER BINDING PROTEIN; FLAVODOXIN; GLOBIN; MYOGLOBIN; PHYCOCYANIN; PLASTOCYANIN; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; CONTROLLED STUDY; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 0029982530     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050711     Document Type: Article

References (38)

1. Adman ET. 1985. Structure and function of small blue copper proteins. In: Harrison P, ed. Metalloproteins, part I. London: Macmillan. pp 1-42.
2. Blundell TL, Johnson MS. 1993. Catching a common fold. Protein Sci 2: 877-883.
3. Bowie JU, Luethy R, Eisenberg D 1991. A method to identify protein sequences that fold into a known three dimensional structure. Science 253:164-170.
4. CATH. 1995. Protein structure classification. London. UC BSM. http: //www.biochem.ucl.ac.uk/bsm/cath/.
5. Chothia C. 1992. Proteins. One thousand families for the molecular biologist. Nature 357:543-544.
6. Chothia C, Lesk AM. 1982. Evolution of proteins formed by β-sheets. I. Plastocyanin and azurin. J Mol Biol 160:309-324.
7. DALI. 1995. Protein structure comparison by alignment of distance matrices. Heidleberg. http://www.embl-heidelber.de/dali/.
8. Finkelstein AV, Ptitsyn OB. 1987. Why do globular proteins fit the limited set of folding patterns? Prog Biophys Mol Biol 50:171-190.
9. Fischer D, Bachar O, Nussinov R, Wolfson H. 1992. An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins. J Biomol Struct Dyn 9:769-789.
10. Fischer D, Tsai CJ, Nussinov R, Wolfson H. 1995. A 3D sequence independent representation of the Protein Data Bank. Protein Eng 8:981-997.
11. Genetics Computer Group. 1991. Program manual for the GCC package, version 7, Madison, WI.
12. Gerstein M, Sonnhammer E, Chothia C. 1994. Volume changes on protein evolution. J Mol Biol 236:1067-1078.
13. Godzik A, Skolnick J. 1994. Flexible algorithm for direct multiple alignment of protein structures and sequences. CABIOS 10:587-596.
14. Godzik A, Skolnick J, Kolinski A. 1992. A topology fingerprint approach to the inverse folding problem. J Mol Biol 227:227-238.
15. Godzik A, Skolnick J, Kolinski A. 1993. Regularities in interaction patterns of globular proteins. Protein Eng 6:801-810.
16. Gribskov M, Dereveux J. 1991. Sequence analysis primer. New York: Stocton Press.
17. Holm L, Sander C. 1993. Protein structure comparison by alignment of distance matrices. J Mol Biol 233:123-138.
18. Jones DT, Taylor WR, Thornton JM. 1992. A new approach to protein fold recognition. Nature 358:86-89.
19. Kabsch W. 1978. A discussion of the solution of the best rotation to relate two sets of vectors. Acta Crystallogr A 34:827-828.
20. Lathrop RH. 1994. The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng 7:1059-1068.
21. Lemer C, Rooman M, Wodak S. 1995. Protein structure prediction by threading methods: Evaluation of current techniques. Proteins Struct Funct Genet 23:337-355.
22. Lesk AM, Chothia C. 1980. How different amino acid sequences determine similar protein structures. J Mol Biol 156:225-270.
23. Maiorov VN, Crippen GM. 1994. Significance of root-mean square deviation in comparing three-dimensional structures of globular proteins. J Mol Biol 235:625-634.
24. MatchMaker. 1994. MatchMaker 1.0. St. Loius, Missouri: Tripos Associates.
25. May AC, Johnson MS. 1994. Protein structure comparison using a combination of a genetic algorithm, dynamic programing and least-square minimization. Protein Eng 7:475-485
26. Mitchell EM, Arytmiuk PJ, Rice DW, Willet P. 1990. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J Mol Biol 212:151-166.
27. Orengo CA, Flores TP, Jones DT, Taylor WR, Thornton JM. 1993. Recurring structural motifs in proteins with different functions. Curr Biol 3:131-139.
28. Pascarella S, Argos P. 1992. A data bank merging related protein structures and sequences. Protein Eng 5:121-137.
29. Pastore A, Lesk AM. 1990. Comparison of the structure of globins and phycocyanins: Evidence for evolutionary relationship. Proteins Struct Funct Genet 8:133-155.
30. Russell R, Barton G. 1994. Structural features can be unconserved in proteins with similar folds. J Mol Biol 244:332-350.
31. Russell RB, Barton GJ. 1992. Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels. Proteins Struct Funct Genet 14:309-323.
32. Sali A, Blundell TL. 1990. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 212:403-428.
33. Saqi M, Sternberg M. 1991. A simple method to generate non-trivial alternate alignments of protein sequences. J Mol Biol 219:727-732.
34. SCOP. 1995. Structural classification of proteins, http://www.bio.cam.ac. uk/scop.
35. Taylor WR, Orengo CA. 1989. Protein structure alignment. J Mol Biol 208:1-22.
36. Vingron M, Argos P. 1990. Determination of reliable regions in protein sequence alignment. Protein Eng 3:565-569.
37. Vogt G, Etzold T, Argos P. 1995. An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited. J Mol Biol 249:816-831.
38. Zuker M. 1991. Suboptimal sequence alignment in molecular biology. Alignment with error analysis. J Mol Biol 221:403-420.