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- Argos P. A sensitive procedure to compare amino acid sequences. J Mol Biol. 1987 Jan 20;193(2):385–396. doi: 10.1016/0022-2836(87)90226-9. [DOI] [PubMed] [Google Scholar]
- Barton G. J., Sternberg M. J. A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol. 1987 Nov 20;198(2):327–337. doi: 10.1016/0022-2836(87)90316-0. [DOI] [PubMed] [Google Scholar]
- Barton G. J., Sternberg M. J. Flexible protein sequence patterns. A sensitive method to detect weak structural similarities. J Mol Biol. 1990 Mar 20;212(2):389–402. doi: 10.1016/0022-2836(90)90133-7. [DOI] [PubMed] [Google Scholar]
- Bedarkar S., Turnell W. G., Blundell T. L., Schwabe C. Relaxin has conformational homology with insulin. Nature. 1977 Dec 1;270(5636):449–451. doi: 10.1038/270449a0. [DOI] [PubMed] [Google Scholar]
- Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
- Blundell T. L., Sibanda B. L., Sternberg M. J., Thornton J. M. Knowledge-based prediction of protein structures and the design of novel molecules. 1987 Mar 26-Apr 1Nature. 326(6111):347–352. doi: 10.1038/326347a0. [DOI] [PubMed] [Google Scholar]
- Blundell T., Carney D., Gardner S., Hayes F., Howlin B., Hubbard T., Overington J., Singh D. A., Sibanda B. L., Sutcliffe M. 18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design. Eur J Biochem. 1988 Mar 15;172(3):513–520. doi: 10.1111/j.1432-1033.1988.tb13917.x. [DOI] [PubMed] [Google Scholar]
- Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164–170. doi: 10.1126/science.1853201. [DOI] [PubMed] [Google Scholar]
- Chothia C., Lesk A. M. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986 Apr;5(4):823–826. doi: 10.1002/j.1460-2075.1986.tb04288.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chothia C. Proteins. One thousand families for the molecular biologist. Nature. 1992 Jun 18;357(6379):543–544. doi: 10.1038/357543a0. [DOI] [PubMed] [Google Scholar]
- Claessens M., Van Cutsem E., Lasters I., Wodak S. Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng. 1989 Jan;2(5):335–345. doi: 10.1093/protein/2.5.335. [DOI] [PubMed] [Google Scholar]
- Dayhoff M. O., Barker W. C., Hunt L. T. Establishing homologies in protein sequences. Methods Enzymol. 1983;91:524–545. doi: 10.1016/s0076-6879(83)91049-2. [DOI] [PubMed] [Google Scholar]
- Doolittle R. F. Similar amino acid sequences: chance or common ancestry? Science. 1981 Oct 9;214(4517):149–159. doi: 10.1126/science.7280687. [DOI] [PubMed] [Google Scholar]
- Eigenbrot C., Randal M., Quan C., Burnier J., O'Connell L., Rinderknecht E., Kossiakoff A. A. X-ray structure of human relaxin at 1.5 A. Comparison to insulin and implications for receptor binding determinants. J Mol Biol. 1991 Sep 5;221(1):15–21. [PubMed] [Google Scholar]
- Eventoff W., Rossmann M. G. The evolution of dehydrogenases and kinases. CRC Crit Rev Biochem. 1975 Aug;3(2):111–140. doi: 10.3109/10409237509102554. [DOI] [PubMed] [Google Scholar]
- Hubbard T. J., Blundell T. L. Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. 1987 Jun;1(3):159–171. doi: 10.1093/protein/1.3.159. [DOI] [PubMed] [Google Scholar]
- Johnson M. S., Sali A., Blundell T. L. Phylogenetic relationships from three-dimensional protein structures. Methods Enzymol. 1990;183:670–690. doi: 10.1016/0076-6879(90)83044-a. [DOI] [PubMed] [Google Scholar]
- Johnson M. S., Sutcliffe M. J., Blundell T. L. Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins. J Mol Evol. 1990 Jan;30(1):43–59. doi: 10.1007/BF02102452. [DOI] [PubMed] [Google Scholar]
- Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 1992 Jul 2;358(6381):86–89. doi: 10.1038/358086a0. [DOI] [PubMed] [Google Scholar]
- Jones T. A., Thirup S. Using known substructures in protein model building and crystallography. EMBO J. 1986 Apr;5(4):819–822. doi: 10.1002/j.1460-2075.1986.tb04287.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lesk A. M., Levitt M., Chothia C. Alignment of the amino acid sequences of distantly related proteins using variable gap penalties. Protein Eng. 1986 Oct-Nov;1(1):77–78. doi: 10.1093/protein/1.1.77. [DOI] [PubMed] [Google Scholar]
- Louie G. V., Brownlie P. D., Lambert R., Cooper J. B., Blundell T. L., Wood S. P., Warren M. J., Woodcock S. C., Jordan P. M. Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site. Nature. 1992 Sep 3;359(6390):33–39. doi: 10.1038/359033a0. [DOI] [PubMed] [Google Scholar]
- Lüthy R., McLachlan A. D., Eisenberg D. Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins. 1991;10(3):229–239. doi: 10.1002/prot.340100307. [DOI] [PubMed] [Google Scholar]
- Matthews B. W., Rossmann M. G. Comparison of protein structures. Methods Enzymol. 1985;115:397–420. doi: 10.1016/0076-6879(85)15029-9. [DOI] [PubMed] [Google Scholar]
- Murthy M. R. A fast method of comparing protein structures. FEBS Lett. 1984 Mar 12;168(1):97–102. doi: 10.1016/0014-5793(84)80214-8. [DOI] [PubMed] [Google Scholar]
- Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
- Overington J., Johnson M. S., Sali A., Blundell T. L. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci. 1990 Aug 22;241(1301):132–145. doi: 10.1098/rspb.1990.0077. [DOI] [PubMed] [Google Scholar]
- Pascarella S., Argos P. A data bank merging related protein structures and sequences. Protein Eng. 1992 Mar;5(2):121–137. doi: 10.1093/protein/5.2.121. [DOI] [PubMed] [Google Scholar]
- Pickett S. D., Saqi M. A., Sternberg M. J. Evaluation of the sequence template method for protein structure prediction. Discrimination of the (beta/alpha)8-barrel fold. J Mol Biol. 1992 Nov 5;228(1):170–187. doi: 10.1016/0022-2836(92)90499-a. [DOI] [PubMed] [Google Scholar]
- Ponder J. W., Richards F. M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol. 1987 Feb 20;193(4):775–791. doi: 10.1016/0022-2836(87)90358-5. [DOI] [PubMed] [Google Scholar]
- Rao S. T., Rossmann M. G. Comparison of super-secondary structures in proteins. J Mol Biol. 1973 May 15;76(2):241–256. doi: 10.1016/0022-2836(73)90388-4. [DOI] [PubMed] [Google Scholar]
- Richards F. M., Kundrot C. E. Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins. 1988;3(2):71–84. doi: 10.1002/prot.340030202. [DOI] [PubMed] [Google Scholar]
- Richardson J. S. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. doi: 10.1016/s0065-3233(08)60520-3. [DOI] [PubMed] [Google Scholar]
- Russell R. B., Barton G. J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins. 1992 Oct;14(2):309–323. doi: 10.1002/prot.340140216. [DOI] [PubMed] [Google Scholar]
- Sali A., Blundell T. L. 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. 1990 Mar 20;212(2):403–428. doi: 10.1016/0022-2836(90)90134-8. [DOI] [PubMed] [Google Scholar]
- Sali A., Overington J. P., Johnson M. S., Blundell T. L. From comparisons of protein sequences and structures to protein modelling and design. Trends Biochem Sci. 1990 Jun;15(6):235–240. doi: 10.1016/0968-0004(90)90036-b. [DOI] [PubMed] [Google Scholar]
- Sander C., Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991;9(1):56–68. doi: 10.1002/prot.340090107. [DOI] [PubMed] [Google Scholar]
- Sippl M. J. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol. 1990 Jun 20;213(4):859–883. doi: 10.1016/s0022-2836(05)80269-4. [DOI] [PubMed] [Google Scholar]
- Summers N. L., Carlson W. D., Karplus M. Analysis of side-chain orientations in homologous proteins. J Mol Biol. 1987 Jul 5;196(1):175–198. doi: 10.1016/0022-2836(87)90520-1. [DOI] [PubMed] [Google Scholar]
- Sutcliffe M. J., Haneef I., Carney D., Blundell T. L. Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1987 Oct-Nov;1(5):377–384. doi: 10.1093/protein/1.5.377. [DOI] [PubMed] [Google Scholar]
- Sutcliffe M. J., Hayes F. R., Blundell T. L. Knowledge based modelling of homologous proteins, Part II: Rules for the conformations of substituted sidechains. Protein Eng. 1987 Oct-Nov;1(5):385–392. doi: 10.1093/protein/1.5.385. [DOI] [PubMed] [Google Scholar]
- Taylor W. R. Identification of protein sequence homology by consensus template alignment. J Mol Biol. 1986 Mar 20;188(2):233–258. doi: 10.1016/0022-2836(86)90308-6. [DOI] [PubMed] [Google Scholar]
- Taylor W. R., Orengo C. A. A holistic approach to protein structure alignment. Protein Eng. 1989 May;2(7):505–519. doi: 10.1093/protein/2.7.505. [DOI] [PubMed] [Google Scholar]
- Vriend G., Sander C. Detection of common three-dimensional substructures in proteins. Proteins. 1991;11(1):52–58. doi: 10.1002/prot.340110107. [DOI] [PubMed] [Google Scholar]
- Zhu Z. Y., Sali A., Blundell T. L. A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Eng. 1992 Jan;5(1):43–51. doi: 10.1093/protein/5.1.43. [DOI] [PubMed] [Google Scholar]