A knowledge-based architecture for protein sequence analysis and structure prediction

Journal of Molecular Graphics - Tập 8 - Trang 94-107 - 1990
Dominic A. Clark1, Geoffrey J. Barton1, Christopher J. Rawlings1
1Biomedical Computing Unit, Imperial Cancer Research Fund, Lincoln's Inn Fields, London, England

Tài liệu tham khảo

Blundell, 1987, Knowledge-based prediction of protein structures and the design of novel molecules, Nature, 326, 347, 10.1038/326347a0 Sutcliffe, 1987, Knowledge based modelling of homologous proteins, part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures, Protein Eng., 1, 377, 10.1093/protein/1.5.377 Sutcliffe, 1987, Knowledge based modelling of homologous proteins, part II. Rules for the conformation of substituted side-chains, Protein Eng., 1, 385, 10.1093/protein/1.5.385 Fox, 1985, A short account of Knowledge Engineering, Knowledge Eng. Rev., 1, 4, 10.1017/S0269888900000424 1989, 2 Stemberg, 1982, Prediction of the secondary and tertiary structures of interferon from four homologous amino acid sequences, Int. J. Biol. Macromol., 4, 137, 10.1016/0141-8130(82)90042-3 Cohen, 1986, Structure-activity studies of interleukin-2, Science, 234, 349, 10.1126/science.3489989 Cohen, 1987, Prediction of the three-dimensional structure of human growth hormone, PROTEINS: Structure, Function and Genetics, 2, 162, 10.1002/prot.340020209 Hurle, 1987, Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase, PROTEINS: Structure, Function and Genetics, 2, 210, 10.1002/prot.340020306 Crawford, 1987, Prediction of secondary structure by evolutionary comparison: Application to the alpha subunit of tryptophan synthase, PROTEINS: Structure, Function and Genetics, 2, 118, 10.1002/prot.340020206 Fishleigh, 1987, Studies on rationales for an expert system approach to the interpretation of protein sequence data, FEBS Lett., 214, 219, 10.1016/0014-5793(87)80060-1 Taylor, 1989, The predicted secondary structure of the nucleotide-binding sites of six cation-transporting ATPases leads to a probable tertiary fold, Eur. J. Biochem., 179, 241, 10.1111/j.1432-1033.1989.tb14547.x Rawlings, 1985, Reasoning about protein topology using the logic programming language PROLOG, J. Mol. Graphics, 3, 151, 10.1016/0263-7855(85)80027-8 Taylor, 1987, Protein structure prediction Thomton, 1988, The shape of things to come, Nature, 335, 10, 10.1038/335010a0 Rawlings, 1987, Artificial Intelligence and Protein Structure Prediction, 59 Frost, 1986, Knowledge Engineering through Knowledge Programming: The PROPS2 Package, ICRF Technical Report Duncan, 1986, The PROPS2 Reference Manual. ICRF Biomedical Computing Unit Technical Report Clark, 1988, Knowledge Engineering in the CARDS Project: A Review of Work in Progress. ICRF, Biomedical Computing Unit Technical Report Nii, 1986, Blackboard systems: The blackboard model of problem solving and the evolution of blackboard architectures, Al Magazine, 7, 38 Nii, 1986, Blackboard systems: Blackboard application systems, blackboard systems from a Knowledge Engineering perspective, Al Magazine, 7, 82 Engelmore, 1988 Erman, 1980, The Hearsay-II speech-understanding system: Integrating knowledge to resolve uncertainty, Comput. Surveys, 12, 213, 10.1145/356810.356816 Hayes-Roth, 1988, PROTEAN: Deriving protein structure from constraints Terry, 1983, The CRYSALIS Project: Hierarchical Control of Production Systems Terry, 1988, Using explicit strategic knowledge to control expert systems Langlotz, 1984, Adapting a consultation system to critique user plans, 77 Nakai, 1988, Cluster analysis of amino acid indices for prediction of protein structure and function, Protein Eng., 2, 93, 10.1093/protein/2.2.93 Fox, 1986, The PROPS2 Primer, ICRF Biomedical Computing Unit Technical Report Clark, 1978, Negation as failure, 10.1007/978-1-4684-3384-5_11 von, 1986 Fox, 1989, Symbolic decision procedures for knowledge based systems Clark, 1990, Numerical and symbolic approaches to uncertainty management in AI: A review and discussion, AI Rev., 4, 109 Barton, 1987, A strategy for the rapid multiple alignment of protein sequences, J. Mol. Biol., 198, 327, 10.1016/0022-2836(87)90316-0 Barton, 1989, Protein multiple sequence alignment and flexible pattern matching, 183 Garnier, 1978, Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins, J. Mol. Biol., 120, 97, 10.1016/0022-2836(78)90297-8 Gibrat, 1987, Further developments of protein secondary structure prediction using information theory, J. Mol. Biol., 198, 425, 10.1016/0022-2836(87)90292-0 Rawlings, 1988, Designing databases for molecular biology, Nature, 334, 477, 10.1038/334477a0 Clark, 1989, Protein Structure Prediction: Knowledge Engineering in a Large Distributed Domain. ICRF, Biomedical Computing Unit Technical Report Zvelebil, 1987, Prediction of protein secondary structure and active sites using the alignment of homologous sequences, J. Mol. Biol., 195, 957, 10.1016/0022-2836(87)90501-8 Taylor, 1983, Prediction of supersecondary structure in proteins, Nature, 301, 540, 10.1038/301540a0 Biou, 1988, Secondary structure prediction: Combination of three different methods, Protein Eng., 2, 185, 10.1093/protein/2.3.185 Chou, 1974, Prediction of protein conformation, Biochemistry, 13, 222, 10.1021/bi00699a002 Hennessey, 1981, Information content in the circular dichroism of proteins, Biochemistry, 20, 1085, 10.1021/bi00508a007