Derivation of rules for comparative protein modeling from a database of protein structure alignments
Version of Record online: 31 DEC 2008
Copyright © 1994 The Protein Society
Volume 3, Issue 9, pages 1582–1596, September 1994
How to Cite
ŠAli, A. and Overington, J. P. (1994), Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Science, 3: 1582–1596. doi: 10.1002/pro.5560030923
- Issue online: 31 DEC 2008
- Version of Record online: 31 DEC 2008
- Manuscript Accepted: 16 MAY 1994
- Manuscript Received: 8 MAR 1994
- 1987. Protein Data Bank. In: AllenFH, BergerhoffG, SieversR, eds. Crystallographic databases—Information, content, software systems, scientific applications. Bonn/Cambridge/Chester: Data Commission of the International Union of Crystallography. pp 107–132. , , , ,
- 1988. A protein sequence/structure database. Nature 335: 745–746. , , , , , , , , , , , , , .
- 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112: 535–542. , , , , , , , ,
- 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164–170. , ,
- 1969. A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme. J Mol Biol 42: 65–86. , , , , , .
- 1989. PKB: A program system and data base for analysis of protein structure. Proteins Struct Funct Genet 5: 233–247. .
- 1988. The Genbank sequence data bank. Nucleic Acids Res 15: 1861–1864. ,
- 1992. One thousand families for the molecular biologist. Nature 360: 543–544.
- 1986. The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823–826. , .
- 1974. Prediction of protein conformation. Biochemistry 13: 222–245. , .
- 1989. Tertiary structure prediction. In: FasmanGD, ed. Prediction of protein structure and the principles of protein conformation. New York: Plenum Press. pp 647–705. , .
- 1978. In: DayhoffMO, ed. Atlas of protein sequence and structure, vol 5, supp 3. Washington, D.C.: National Biomedical Research Foundation, pp 345–352. , , .
- 1992. X-ray analyses of peptide-inhibitor complexes define the structural basis of specificity for human and mouse renins. Nature 357: 466–472. , , , , , , , , , , , , , , , , , .
- 1993. Prediction of protein sidechain conformations from a backbone conformation dependent rotamer library. J Mol Biol 230: 543–571. ,
- 1991. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A 47: 392–400. ,
- 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783–791.
- 1991. A search for the most stable folds of protein chains. Nature 351: 497–499. , .
- 1990. Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein. Nature 346: 623–628. , , .
- 1986. The protein identification resource. Nucleic Acids Res 14: 11–15. , , .
- 1992. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 227: 227–238. , ,
- 1987. Profile analysis: Detection of distantly related proteins. Proc Natl Acad Sci USA 84: 4355–4358. , ,
- 1986. The EMBL data library. Nucleic Acids Res 14: 5–9. ,
- 1993. How amino-acid insertions are allowed in an alpha-helix of T4 lysozyme. Nature 361: 561–564. , , , .
- 1992. A database of protein structure families with common folding motifs. Protein Sci 1: 1691–1698. , , , ,
- 1987. Comparison of solvent inaccessible cores of homologous proteins: Definitions useful for protein modelling. Protein Eng 1: 159–171. , .
- 1991. SESAM: A relational database for structure and sequence of macromolecules. Proteins Struct Funct Genet 11: 59–76. , , .
- 1989. A relational database of protein structures designed for flexible enquires about conformation. Protein Eng 2: 431–442. , .
- 1978. Conformation of amino acid side-chains in proteins. J Mol Biol 125: 357–386. , , ,
- 1993. Alignment and searching for common protein folds using a data bank of structural templates. J Mol Biol 231: 735–752. , , .
- 1992. A new approach to protein fold recognition. Nature 358: 86–89. , , .
- 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577–2637. ,
- 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283–291. , , , .
- 1992. Assessment of protein models with three-dimensional profiles. Nature 356: 83–85. , ,
- 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. , ,
- 1991. Influence of proline residues on protein conformation. J Mol Biol 218: 397–412. , .
- 1978. Hydrophobic character of amino acid residues in globular proteins. Nature 275: 673–674. , .
- 1985. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18: 534–552. , .
- 1992. Structural basis of latency in plasminogen activator inhibitor-1. Nature 355: 270–273. , , , , , , , .
- 1993. Identification and classification of protein fold families. Protein Eng 6: 485–500. , , , .
- 1992. Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds. Protein Sci 1: 216–226. , , , , .
- 1990. Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction. Proc R Soc Land B 241: 132–145. , , , .
- 1993. Molecular recognition in protein families: A database of aligned three-dimensional structures of related proteins. Biochem Soc Trans 21: 597–604. , , , , , , .
- 1986. Computer-aided model-building strategies for protein design. Biochemistry 25: 5987–5991. , .
- 1992. A data bank merging related protein structures and sequences. Protein Eng 5: 121–137. ,
- 1987. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193: 775–791. , .
- 1992. Numerical recipes, 2nd ed. Cambridge, UK: Cambridge University Press. , , , .
- 1993. Energetics of the disulphide bridge: An ab initio study. Biopolymers 33: 1591–1603. ,
- 1981. The anatomy and taxonomy of protein structure. Adv Protein Chem 34: 167–339. .
- 1988. Amino acid preferences for specific locations at the ends of α-helices. Science 240: 1648–1652. , .
- 1978. Packing of α-helices: Geometrical constraints and contact areas. J Mol Biol 119: 537–555. , .
- 1991. Modelling three-dimensional structure of proteins from their sequence of amino acid residues [thesis]. London: University of London.
- 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. , .
- 1993. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779–815. , .
- 1990. From comparisons of protein sequences and structures to protein modelling and design. Trends Biochem Sci 15: 235–240. , , , .
- 1993. Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 230: 592–612. , ,
- 1990. 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 213: 859–883. .
- 1992. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins Struct Funct Genet 13: 258–271. ,
- 1993. Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and endothelin. Protein Eng 6: 873–882. , ,
- 1989. Stereochemical modeling of disulphide bridges. Criteria for introduction into proteins by site-directed mutagenesis. Protein Eng 3: 95–103. , , , , ,
- 1990. Occurrence and role of cis peptide bonds in protein structures. J Mol Biol 214: 253–260. , , .
- 1987. Knowledge based modelling of homologous proteins, Part I: Three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1: 377–384. , , , .
- 1991. Towards protein tertiary fold prediction using distance and motif constraints. Protein Eng 4: 853–870. .
- 1981. Disulphide bridges in globular proteins. J Mol Biol 151: 261–287. .
- 1990. Protein motifs and data-base searching. In: BradshawRA, PurtonM, eds. Proteins: Form and function. Cambridge, UK: Elsevier Science Publishers. pp 153–161. , .
- 1993. Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. J Mol Biol 229: 194–220. , , , , , .
- 1990. β-Turns and their distortions: A proposed new nomenclature. Protein Eng 3: 479–493. , .
- 1992. A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Eng 5: 43–51. , , .