Amino acid pair interchanges at spatially conserved locations

Journal of Molecular Biology

Volumn 256, Issue 5, 1996, Pages 924-938

  Naor, Dalit ^a   Fischer, Daniel ^a,d   Jernigan, Robert L ^b   Wolfson, Haim J ^a   Nussinov, Ruth ^a,c  

^a TEL AVIV UNIVERSITY   (Israel)

^b NATIONAL CANCER INSTITUTE   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Amino acid conservation; Amino acid interchanges; Geometric hashing; Structural motifs; Structure comparison

Indexed keywords

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COMPARATIVE STUDY; GENETIC CONSERVATION; GEOMETRY; HYDROPHILICITY; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN STABILITY; PUNISHMENT;

EID: 0029986889     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0138     Document Type: Article

References (23)

1. Altschul, S. F. (1991). Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219, 555-565.
2. Bachar, O., Fischer, D., Nussinov, R. & Wolfson, H. J. (1993). A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng. 6 (3), 279-288.
3. Dayhoff, M., Schwartz, R. M. & Orcutt, B. C. (1978). A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure (Dayhoff, M., ed.), vol. 5, pp. 345-352. National Biomedical Research Foundation Silver Spring, MD. Supplement 3.
4. Doolittle, R. F. (1994). Convergent evolution: the need to be explicit. Trends BioSci. 19, 15-18.
5. Fischer, D., Lin, S. L., Wolfson, H. J. & Nussinov, R. (1994). 3-d, sequence-order independent structural comparison of trypsin against the crystallographic database reveals active site similarities to subtilisin-like and sulfhydryl proteases: potential implications. Protein Sci. 3, 769-778.
6. Fischer, D., Tsai, C. J., Nussinov, R. & Wolfson, H. J. (1995). A 3-d sequence independent representation of the protein databank. Protein Eng. 8, 981-997.
7. Gonnet, G. H., Cohen, M. A. & Benner, S. A. (1992). Exhaustive matching of the entire protein sequence database. Science, 256, 1443-1445.
8. Henikoff, S. & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
9. Huang, E. S., Subbiah, S. & Levitt, M. (1995). Recognizing native folds by the arrangement of hydrophobic and polar residues. J. Mol. Biol. 252, 709-720.
10. Johnson, M. S., Overington, J. P. & Blundell, T. L. (1993). Alignment and searching for common protein folds using a data bank of structural templates. J. Mol. Biol. 231, 735-752.
11. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. CABIOS, 8 (3), 275-282.
12. Lamdan, Y, Schwartz, J. T. & Wolfson, H. J. (1990). Affine invariant model-based object recognition. IEEE Trans. Robot. Automat. 6, 578-589.
13. Luthy R., McLachlan, A. D. & Eisenberg, D. (1991). Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins: Struct. Funct. Genet. 10, 229-239.
14. Miyazawa, S. & Jernigan, R. L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18 (3), 534-552.
15. Miyazawa, S. & Jernigan, R. L. (1993). A new substitution matrix for protein sequence searches based on contact frequencies in protein structure. Protein Eng. 6 (3), 267-278.
16. Nussinov, R. & Wolfson, H. J. (1991). Efficient detection of three-dimensional motifs in biological macromolecules by computer vision techniques. Proc. Natl Acad. Sci. USA, 88, 10495-10499.
17. Overington, J., Donnelly D., Johnson, M. J., Sali, A. & Blundell, T. (1992). Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci. 18, 216-226.
18. Risler, J. L., Delorme, M. O., Delacroix, H. & Henaut, A. (1988). Amino acid substitutions in structurally related proteins: a pattern recognition approach. J. Mol. Biol. 204, 1019-1029.
19. Shrake, A. & Rupley, J. A. (1973). Environment and exposure to solvent of protein atoms. J. Mol. Biol. 79, 351-371.
20. Swanson, R. (1984). A vector representation for amino acid sequences. Bull. Math. Biol. 46 (4), 623-639.
21. Taylor, W. R. (1986). The classification of amino acid conservation. J. Theoret. Biol. 119, 205-218.
22. 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.
23. Yue, Y. K. & Dill, K. A. (1992). Inverse protein folding problem: designing polymer sequences. Proc. Natl Acad. Sci. USA, 89, 4163-4167.