330 results found
Sternberg MJE, Hirst JD, Lewis RA, et al., 1994, Application of machine learning to protein structure prediction and drug design, ISSN: 0963-3308
The use of inductive-based logic programming (ILP) in predicting protein structure and drug design was discussed in this article. In the study of alpha and beta fields with alternating alpha-helices and beta-sheet strands, ILP program GOLEM was employed. GOLEM was capable of generating an inductive hypothesis based on coded facts and negative counter-example and chemical background knowledge. However, for drug design machine learning program PROLOG was applied. PROLOG can comprehend the properties of bonds and atoms. It can also give insight in the chemical principles of aromatic and heteroaromatic nitro compounds. In conclusion, machine learning ILP programs can greatly enhance biochemical developments.
King RD, Clark DA, Shirazi J, et al., 1994, Inductive logic programming used to discover topological constraints in protein structures., Proc Int Conf Intell Syst Mol Biol, Vol: 2, Pages: 219-226, ISSN: 1553-0833
This paper describes the application of the Inductive Logic Programming (ILP) program GOLEM to the discovery of constraints in the packing of beta-sheets in alpha/beta proteins. These constraints (rules) have a role in understanding the protein folding problem. Constraints were learnt for four features of beta-sheet packing: the winding direction of two sequential strands, whether two consecutive strands pack parallel or anti-parallel, whether two strands pack adjacently, and whether a beta-strand is at an edge. Investigation of the learnt constraints revealed interesting patterns, some of which were previously known, others that were novel. Novel features include the discovery: that the relationship between pairs of sequential strands is in general one of decreasing size, and that more sequential pairs of strands wind in the direction out than the direction in. We conclude that machine learning has a useful place in molecular biology as a pattern discovery tool.
JACKSON RM, STERNBERG MJE, 1993, PROTEIN SURFACE-AREA DEFINED, NATURE, Vol: 366, Pages: 638-638, ISSN: 0028-0836
King RD, Hirst JD, Sternberg MJE, 1993, New approaches to QSAR: Neural networks and machine learning, Perspectives in Drug Discovery and Design, Vol: 1, Pages: 279-290, ISSN: 0928-2866
Neural networks and machine learning are two methods that are increasingly being used to model QSARs. They make few statistical assumptions and are nonlinear and nonparametric. We describe back-propagation from the field of neural networks, and GOLEM from machine learning, and illustrate their learning mechanisms using a simple expository problem. Back-propagation and GOLEM are then compared with multiple linear regression (using the parameters and their squares) on two real drug design problems: the inhibition of Escherichia coli dihydrofolate reductase (DHFR) by pyrimidines and the inhibition of rat/mouse tumour DHFR by triazines. © 1993 ESCOM Science Publishers B.V.
LOFTS FJ, HURST HC, STERNBERG MJE, et al., 1993, SPECIFIC SHORT TRANSMEMBRANE SEQUENCES CAN INHIBIT TRANSFORMATION BY THE MUTANT NEU GROWTH-FACTOR RECEPTOR IN-VITRO AND IN-VIVO, ONCOGENE, Vol: 8, Pages: 2813-2820, ISSN: 0950-9232
BAX B, BLABER M, FERGUSON G, et al., 1993, PREDICTION OF THE 3-DIMENSIONAL STRUCTURES OF THE NERVE GROWTH-FACTOR AND EPIDERMAL GROWTH-FACTOR BINDING-PROTEINS (KALLIKREINS) AND AN HYPOTHETICAL STRUCTURE OF THE HIGH-MOLECULAR-WEIGHT COMPLEX OF EPIDERMAL GROWTH-FACTOR WITH ITS BINDING-PROTEIN, PROTEIN SCIENCE, Vol: 2, Pages: 1229-1241, ISSN: 0961-8368
HIRST JD, STERNBERG MJE, 1993, PREDICTION OF ATP-BINDING MOTIFS - A COMPARISON OF A PERCEPTRON-TYPE NEURAL-NETWORK AND A CONSENSUS SEQUENCE METHOD (VOL 4, PG 615, 1991), PROTEIN ENGINEERING, Vol: 6, Pages: 549-554, ISSN: 0269-2139
MUGGLETON S, KING RD, STERNBERG MJE, 1993, PROTEIN SECONDARY STRUCTURE PREDICTION USING LOGIC-BASED MACHINE LEARNING, PROTEIN ENGINEERING, Vol: 6, Pages: 549-549, ISSN: 0269-2139
PICKETT SD, STERNBERG MJE, 1993, EMPIRICAL SCALE OF SIDE-CHAIN CONFORMATIONAL ENTROPY IN PROTEIN-FOLDING, JOURNAL OF MOLECULAR BIOLOGY, Vol: 231, Pages: 825-839, ISSN: 0022-2836
BAUM H, BUTLER P, DAVIES H, et al., 1993, AUTOIMMUNE-DISEASE AND MOLECULAR MIMICRY - AN HYPOTHESIS, TRENDS IN BIOCHEMICAL SCIENCES, Vol: 18, Pages: 140-144, ISSN: 0968-0004
BATES PA, ISLAM SA, STERNBERG MJE, 1993, STRUCTURE OF DEBRISOQUINIUM SULFATE, ACTA CRYSTALLOGRAPHICA SECTION C-CRYSTAL STRUCTURE COMMUNICATIONS, Vol: 49, Pages: 300-303, ISSN: 0108-2701
ADZHUBEI AA, STERNBERG MJE, 1993, LEFT-HANDED POLYPROLINE-II HELICES COMMONLY OCCUR IN GLOBULAR-PROTEINS, JOURNAL OF MOLECULAR BIOLOGY, Vol: 229, Pages: 472-493, ISSN: 0022-2836
Sternberg MJE, 1993, Corrigendum: Protein secondary structure prediction using logic-based machine learning (Protein Engineering (1993) 5 (647-657)), Protein Engineering, Vol: 6, ISSN: 0269-2139
Hirst JD, Sternberg MJE, 1993, Corrigendum: Prediction of ATP/GTP-bindmg motifs: A comparison of a perceptron type neural network and a consensus sequence method (Protein Engineering (1993) 4 (615-623)), Protein Engineering, Vol: 6, ISSN: 0269-2139
© 1993 IEEE. Determining the quantitative structure-activity relationship (QSAR) of a related series of drugs is a central aspect of the drug design process. The machine learning program Golem from the field of inductive logic programming (ILP) applied to QSAR. ILP is the most suitable machine learning technique because it can represent the structural and relational aspects of drugs. A five-step methodology for using machine learning in drug design is presented that consists of identification of the problem, choice of a representation, induction, interpretation of results, and synthesis of new drugs.
HIRST JD, STERNBERG MJE, 1993, QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS OF DIHYDROFOLATE-REDUCTASE INHIBITORS BY NEURAL NETWORKS, PROTEIN ENGINEERING, Vol: 6, Pages: 107-107, ISSN: 0269-2139
ADZHUBEI AA, STERNBERG MJE, 1993, LEFT-HANDED POLYPROLINE-II HELICES AS AN ELEMENT IN PROTEIN-STRUCTURE PREDICTION, PROTEIN ENGINEERING, Vol: 6, Pages: 125-125, ISSN: 0269-2139
KING RD, MUGGLETON S, LEWIS RA, et al., 1992, DRUG DESIGN BY MACHINE LEARNING - THE USE OF INDUCTIVE LOGIC PROGRAMMING TO MODEL THE STRUCTURE-ACTIVITY-RELATIONSHIPS OF TRIMETHOPRIM ANALOGS BINDING TO DIHYDROFOLATE-REDUCTASE, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 89, Pages: 11322-11326, ISSN: 0027-8424
PICKETT SD, SAQI MAS, STERNBERG MJE, 1992, EVALUATION OF THE SEQUENCE TEMPLATE METHOD FOR PROTEIN-STRUCTURE PREDICTION - DISCRIMINATION OF THE (BETA/ALPHA)8-BARREL FOLD, JOURNAL OF MOLECULAR BIOLOGY, Vol: 228, Pages: 170-187, ISSN: 0022-2836
WALLS PH, STERNBERG MJE, 1992, NEW ALGORITHM TO MODEL PROTEIN PROTEIN RECOGNITION BASED ON SURFACE COMPLEMENTARITY - APPLICATIONS TO ANTIBODY ANTIGEN DOCKING, JOURNAL OF MOLECULAR BIOLOGY, Vol: 228, Pages: 277-297, ISSN: 0022-2836
MUGGLETON S, KING RD, STERNBERG MJE, 1992, PROTEIN SECONDARY STRUCTURE PREDICTION USING LOGIC-BASED MACHINE LEARNING, PROTEIN ENGINEERING, Vol: 5, Pages: 647-657, ISSN: 0269-2139
HIRST JD, STERNBERG MJE, 1992, PREDICTION OF STRUCTURAL AND FUNCTIONAL FEATURES OF PROTEIN AND NUCLEIC-ACID SEQUENCES BY ARTIFICIAL NEURAL NETWORKS, BIOCHEMISTRY, Vol: 31, Pages: 7211-7218, ISSN: 0006-2960
SAQI MAS, BATES PA, STERNBERG MJE, 1992, TOWARDS AN AUTOMATIC METHOD OF PREDICTING PROTEIN-STRUCTURE BY HOMOLOGY - AN EVALUATION OF SUBOPTIMAL SEQUENCE ALIGNMENTS, PROTEIN ENGINEERING, Vol: 5, Pages: 305-311, ISSN: 0269-2139
BATES PA, LUO JC, STERNBERG MJE, 1992, A PREDICTED 3-DIMENSIONAL STRUCTURE FOR THE CARCINOEMBRYONIC ANTIGEN (CEA), FEBS LETTERS, Vol: 301, Pages: 207-214, ISSN: 1873-3468
BERENDT AR, MCDOWALL A, CRAIG AG, et al., 1992, THE BINDING-SITE ON ICAM-1 FOR PLASMODIUM-FALCIPARUM INFECTED ERYTHROCYTES OVERLAPS, BUT IS DISTINCT FROM, THE LFA-1-BINDING SITE, CELL, Vol: 68, Pages: 71-81, ISSN: 0092-8674
STERNBERG MJE, LEWIS RA, KING RD, et al., 1992, MODELING THE STRUCTURE AND FUNCTION OF ENZYMES BY MACHINE LEARNING, FARADAY DISCUSSIONS, Vol: 93, Pages: 269-280, ISSN: 1359-6640
GULLICK WJ, BOTTOMLEY AC, LOFTS FJ, et al., 1992, 3-DIMENSIONAL STRUCTURE OF THE TRANSMEMBRANE REGION OF THE PROTOONCOGENIC AND ONCOGENIC FORMS OF THE NEU PROTEIN, EMBO JOURNAL, Vol: 11, Pages: 43-48, ISSN: 0261-4189
Sternberg MJE, 1992, Secondary structure prediction. Current Opinion in Structural Biology 1992, 2:237-241, Current Opinion in Structural Biology, Vol: 2, Pages: 237-241, ISSN: 0959-440X
The prediction of protein secondary structure from sequence is routinely used whenever a new protein is cloned, and can be the first step in a tertiary structure prediction. This review summarizes the new methods that have been applied during the past year to this long-standing problem. The accuracy for a prediction of α-helices, β-sheets and coil remains at ∼65%. © 1992.
Rees AR, Wetzel R, Sternberg MJE, 1992, Protein Engineering - A Practical Approach, Oxford, Publisher: Oxford University Press
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