Imperial College London

ProfessorMichaelSternberg

Faculty of Natural SciencesDepartment of Life Sciences

Director Centre for Bioinformatics
 
 
 
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Contact

 

+44 (0)20 7594 5212m.sternberg Website

 
 
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Location

 

306Sir Ernst Chain BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

326 results found

Strynadka NCJ, Eisenstein M, KatchalskiKatzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MNGet al., 1996, Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase, NATURE STRUCTURAL BIOLOGY, Vol: 3, Pages: 233-239, ISSN: 1072-8368

JOURNAL ARTICLE

Russell RB, Sternberg MJE, 1996, A novel binding site in catalase is suggested by structural similarity to the calycin superfamily, PROTEIN ENGINEERING, Vol: 9, Pages: 107-111, ISSN: 0269-2139

JOURNAL ARTICLE

King RD, Muggleton SH, Srinivasan A, Sternberg MJEet al., 1996, Structure-activity relationships derived by machine learning: The use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 93, Pages: 438-442, ISSN: 0027-8424

JOURNAL ARTICLE

Bates PA, Jackson RM, Sternberg MJE, 1996, Prediction of protein structures and their docking, 7th SmithKline-Beecham International Symposium on Genomes, Molecular Biology and Drug Discovery, Publisher: ACADEMIC PRESS LTD, Pages: 73-86

CONFERENCE PAPER

King RD, Srinivasan A, Sternberg MJE, 1996, Relating chemical activity to structure: An examination of ILP successes (vol 13, pg 411, 1995), NEW GENERATION COMPUTING, Vol: 14, Pages: 109-109, ISSN: 0288-3635

JOURNAL ARTICLE

Sternberg MJE, 1996, Protein Structure Prediction - A Practical Approach, Oxford, Publisher: Oxford University Press

BOOK

ELLIS SW, HAYHURST GP, SMITH G, LIGHTFOOT T, WONG MMS, SIMULA AP, ACKLAND MJ, STERNBERG MJE, LENNARD MS, TUCKER GT, WOLF CRet al., 1995, EVIDENCE THAT ASPARTIC-ACID-301 IS A CRITICAL SUBSTRATE-CONTACT RESIDUE IN THE ACTIVE-SITE OF CYTOCHROME-P450 2D6, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 270, Pages: 29055-29058, ISSN: 0021-9258

JOURNAL ARTICLE

DOIG AJ, STERNBERG MJE, 1995, SIDE-CHAIN CONFORMATIONAL ENTROPY IN PROTEIN-FOLDING, PROTEIN SCIENCE, Vol: 4, Pages: 2247-2251, ISSN: 0961-8368

JOURNAL ARTICLE

CHICKOS JS, STERNBERG MJE, 1995, A TEST OF THE APPLICABILITY OF SMALL-MOLECULE GROUP ADDITIVITY PARAMETERS IN THE ESTIMATION OF FUSION ENTROPIES OF MACROMOLECULES, THERMOCHIMICA ACTA, Vol: 264, Pages: 13-26, ISSN: 0040-6031

JOURNAL ARTICLE

JACKSON RM, STERNBERG MJE, 1995, A CONTINUUM MODEL FOR PROTEIN-PROTEIN INTERACTIONS - APPLICATION TO THE DOCKING PROBLEM, JOURNAL OF MOLECULAR BIOLOGY, Vol: 250, Pages: 258-275, ISSN: 0022-2836

JOURNAL ARTICLE

ISLAM SA, LUO JC, STERNBERG MJE, 1995, IDENTIFICATION AND ANALYSIS OF DOMAINS IN PROTEINS, PROTEIN ENGINEERING, Vol: 8, Pages: 513-525, ISSN: 0269-2139

JOURNAL ARTICLE

RUSSELL RB, STERNBERG MJE, 1995, STRUCTURE PREDICTION - HOW GOOD ARE WE, CURRENT BIOLOGY, Vol: 5, Pages: 488-490, ISSN: 0960-9822

JOURNAL ARTICLE

STERNBERG MJE, MUGGLETON S, SHRINIVASAN A, 1995, DRUG DESIGN BY MACHINE LEARNING, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol: 209, Pages: 165-COMP, ISSN: 0065-7727

JOURNAL ARTICLE

KING RD, HIRST JD, STERNBERG MJE, 1995, COMPARISON OF ARTIFICIAL-INTELLIGENCE METHODS FOR MODELING PHARMACEUTICAL QSARS, APPLIED ARTIFICIAL INTELLIGENCE, Vol: 9, Pages: 213-233, ISSN: 0883-9514

JOURNAL ARTICLE

KING RD, STERNBERG MJE, SRINIVASAN A, 1995, RELATING CHEMICAL ACTIVITY TO STRUCTURE - AN EXAMINATION OF ILP SUCCESSES, NEW GENERATION COMPUTING, Vol: 13, Pages: 411-433, ISSN: 0288-3635

JOURNAL ARTICLE

Sternberg MJ, Hegyi H, Islam SA, Luo J, Russell RBet al., 1995, Towards an intelligent system for the automatic assignment of domains in globular proteins., Proc Int Conf Intell Syst Mol Biol, Vol: 3, Pages: 376-383, ISSN: 1553-0833

The automatic identification of protein domains from coordinates is the first step in the classification of protein folds and hence is required for databases to guide structure prediction. Most algorithms encode a single concept based and sometimes do not yield assignments that are consistent with the generally accepted perception. Our development of an automatic approach to identify reliably domains from protein coordinates is described. The algorithm is benchmarked against a manual identification of the domains in 284 representative protein chains. The first step is the domain assignment by distance (DAD) algorithm that considers the density of inter-residue contacts represented in a contact matrix. The algorithm yields 85% agreement with the manual assignment. The paper then considers how the reliability of these assignments could be evaluated. Finally the use of structural comparisons using the STAMP algorithm to validate domain assignment is reported on a test case.

JOURNAL ARTICLE

HARRISON PM, STERNBERG MJE, 1994, ANALYSIS AND CLASSIFICATION OF DISULFIDE CONNECTIVITY IN PROTEINS - THE ENTROPIC EFFECT OF CROSS-LINKAGE, JOURNAL OF MOLECULAR BIOLOGY, Vol: 244, Pages: 448-463, ISSN: 0022-2836

JOURNAL ARTICLE

ADZHUBEI AA, STERNBERG MJE, 1994, CONSERVATION OF POLYPROLINE-II HELICES IN HOMOLOGOUS PROTEINS - IMPLICATIONS FOR STRUCTURE PREDICTION BY MODEL-BUILDING, PROTEIN SCIENCE, Vol: 3, Pages: 2395-2410, ISSN: 0961-8368

JOURNAL ARTICLE

KING RD, CLARK DA, SHIRAZI J, STERNBERG MJEet al., 1994, ON THE USE OF MACHINE LEARNING TO IDENTIFY TOPOLOGICAL RULES IN THE PACKING OF BETA-STRANDS, PROTEIN ENGINEERING, Vol: 7, Pages: 1295-1303, ISSN: 0269-2139

JOURNAL ARTICLE

STERNBERG MJE, MUGGLETON S, SHRINIVASAN A, 1994, DRUG DESIGN BY MACHINE LEARNING, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol: 208, Pages: 138-COMP, ISSN: 0065-7727

JOURNAL ARTICLE

HIRST JD, KING RD, STERNBERG MJE, 1994, QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS BY NEURAL NETWORKS AND INDUCTIVE LOGIC PROGRAMMING .1. THE INHIBITION OF DIHYDROFOLATE-REDUCTASE BY PYRIMIDINES, JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, Vol: 8, Pages: 405-420, ISSN: 0920-654X

JOURNAL ARTICLE

HIRST JD, KING RD, STERNBERG MJE, 1994, QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS BY NEURAL NETWORKS AND INDUCTIVE LOGIC PROGRAMMING .2. THE INHIBITION OF DIHYDROFOLATE-REDUCTASE BY TRIAZINES, JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, Vol: 8, Pages: 421-432, ISSN: 0920-654X

JOURNAL ARTICLE

STERNBERG MJE, KING RD, LEWIS RA, MUGGLETON Set al., 1994, APPLICATION OF MACHINE LEARNING TO STRUCTURAL MOLECULAR-BIOLOGY, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES, Vol: 344, Pages: 365-371, ISSN: 0962-8436

JOURNAL ARTICLE

JACKSON RM, STERNBERG MJE, 1994, APPLICATION OF SCALED PARTICLE THEORY TO MODEL THE HYDROPHOBIC EFFECT - IMPLICATIONS FOR MOLECULAR ASSOCIATION AND PROTEIN STABILITY, PROTEIN ENGINEERING, Vol: 7, Pages: 371-383, ISSN: 0269-2139

JOURNAL ARTICLE

SAQI MAS, STERNBERG MJE, 1994, IDENTIFICATION OF SEQUENCE MOTIFS FROM A SET OF PROTEINS WITH RELATED FUNCTION, PROTEIN ENGINEERING, Vol: 7, Pages: 165-171, ISSN: 0269-2139

JOURNAL ARTICLE

STERNBERG MJE, CHICKOS JS, 1994, PROTEIN SIDE-CHAIN CONFORMATIONAL ENTROPY DERIVED FROM FUSION DATA - COMPARISON WITH OTHER EMPIRICAL SCALES, PROTEIN ENGINEERING, Vol: 7, Pages: 149-155, ISSN: 0269-2139

JOURNAL ARTICLE

Sternberg MJE, Hirst JD, Lewis RA, King RD, Srinivasan A, Muggleton Set 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.

CONFERENCE PAPER

King RD, Clark DA, Shirazi J, Sternberg MJet 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.

JOURNAL ARTICLE

JACKSON RM, STERNBERG MJE, 1993, PROTEIN SURFACE-AREA DEFINED, NATURE, Vol: 366, Pages: 638-638, ISSN: 0028-0836

JOURNAL ARTICLE

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.

JOURNAL ARTICLE

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