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

321 results found

Luo JC, Islam SA, Russell RB, Sternberg MJEet al., 1998, A world-wide web server of protein domain assignment, 4th Chinese Peptide Symposium (CPS-96), Publisher: SPRINGER, Pages: 235-236

CONFERENCE PAPER

Muggleton S, Srinivasan A, King RD, Sternberg MJEet al., 1998, Biochemical knowledge discovery using inductive logic programming, 1st International Conference on Discovery Science (DS 98), Publisher: SPRINGER-VERLAG BERLIN, Pages: 326-341, ISSN: 0302-9743

CONFERENCE PAPER

Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJEet al., 1998, Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction, JOURNAL OF MOLECULAR BIOLOGY, Vol: 279, Pages: 1193-1210, ISSN: 0022-2836

JOURNAL ARTICLE

Russell RB, Saqi MAS, Bates PA, Sayle RA, Sternberg MJEet al., 1998, Recognition of analogous and homologous protein folds - assessment of prediction success and associated alignment accuracy using empirical substitution matrices, PROTEIN ENGINEERING, Vol: 11, Pages: 1-9, ISSN: 0269-2139

JOURNAL ARTICLE

Russell RB, Sasieni PD, Sternberg MJE, 1998, Supersites within superfolds. Binding site similarity in the absence of homology, JOURNAL OF MOLECULAR BIOLOGY, Vol: 282, Pages: 903-918, ISSN: 0022-2836

JOURNAL ARTICLE

Saqi MAS, Russell RB, Sternberg MJE, 1998, Misleading local sequence alignments: implications for comparative protein modelling, PROTEIN ENGINEERING, Vol: 11, Pages: 627-630, ISSN: 0269-2139

JOURNAL ARTICLE

Sternberg MJ, Aloy P, Gabb HA, Jackson RM, Moont G, Querol E, Aviles FXet al., 1998, A computational system for modelling flexible protein-protein and protein-DNA docking., Proc Int Conf Intell Syst Mol Biol, Vol: 6, Pages: 183-192, ISSN: 1553-0833

A computational system is described that predicts the structure of protein/protein and protein/DNA complexes starting from unbound coordinate sets. The approach is (i) a global search with rigid-body docking for complexes with shape complementarity and favourable electrostatics; (ii) use of distance constraints from experimental (or predicted) knowledge of critical residues; (iii) use of pair potential to screen docked complexes and (iv) refinement and further screening by protein-side chain optimisation and interfacial energy minimisation. The system has been applied to model ten protein/protein and eight protein-repressor/DNA (steps i to iii only) complexes. In general a few complexes, one of which is close to the true structure, can be generated.

JOURNAL ARTICLE

Sternberg MJE, Gabb HA, Jackson RM, 1998, Predictive docking of protein-protein and protein-DNA complexes, CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 8, Pages: 250-256, ISSN: 0959-440X

JOURNAL ARTICLE

Turcotte M, Muggleton SH, Sternberg MJE, 1998, Application of inductive logic programming to discover rules governing the three-dimensional topology of protein structure, Pages: 53-64, ISSN: 0302-9743

© Springer-Verlag Berlin Heidelberg 1998. Inductive Logic Programming (ILP) has been applied to discover rules governing the three-dimensional topology of protein structure. The data-set unifies two sources of information; SCOP and PROMOTIF. Cross-validation results for experiments using two background knowledge sets, global (attribute-valued) and constitutional (relational), are presented. The application makes use of a new feature of Progol4.4 for numeric parameter estimation. At this early stage of development, the rules produced can only be applied to proteins for which the secondary structure is known. However, since the rules are insightful, they should prove to be helpful in assisting the development of taxonomic schemes. The application of ILP to fold recognition represents a novel and promising approach to this problem.

CONFERENCE PAPER

Zhang XD, Morera S, Bates PA, Whitehead PC, Coffer AI, Hainbucher K, Nash RA, Sternberg MJE, Lindahl T, Freemont PSet al., 1998, Structure of an XRCC1 BRCT domain: a new protein-protein interaction module, EMBO JOURNAL, Vol: 17, Pages: 6404-6411, ISSN: 0261-4189

JOURNAL ARTICLE

Bates PA, Jackson RM, Sternberg MJE, 1997, Model building by comparison: A combination of expert knowledge and computer automation, PROTEINS-STRUCTURE FUNCTION AND GENETICS, Pages: 59-67, ISSN: 0887-3585

JOURNAL ARTICLE

Gabb HA, Jackson RM, Sternberg MJE, 1997, Modelling protein docking using shape complementarity, electrostatics and biochemical information, JOURNAL OF MOLECULAR BIOLOGY, Vol: 272, Pages: 106-120, ISSN: 0022-2836

JOURNAL ARTICLE

King RD, Saqi M, Sayle R, Sternberg MJEet al., 1997, DSC: public domain protein secondary structure prediction, COMPUTER APPLICATIONS IN THE BIOSCIENCES, Vol: 13, Pages: 473-474, ISSN: 0266-7061

JOURNAL ARTICLE

Lohmeyer M, Harrison PM, Kannan S, DeSantis M, OReilly NJ, Sternberg MJE, Salomon DS, Gullick WJet al., 1997, Chemical synthesis, structural modeling, and biological activity of the epidermal growth factor-like domain of human Cripto, BIOCHEMISTRY, Vol: 36, Pages: 3837-3845, ISSN: 0006-2960

JOURNAL ARTICLE

Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJEet al., 1997, An automated classification of the structure of protein loops, JOURNAL OF MOLECULAR BIOLOGY, Vol: 266, Pages: 814-830, ISSN: 0022-2836

JOURNAL ARTICLE

Russell RB, Saqi MAS, Sayle RA, Bates PA, Sternberg MJEet al., 1997, Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation, JOURNAL OF MOLECULAR BIOLOGY, Vol: 269, Pages: 423-439, ISSN: 0022-2836

JOURNAL ARTICLE

Russell RB, Sternberg MJE, 1997, Two new examples of protein structural similarities within the structure-function twilight zone, PROTEIN ENGINEERING, Vol: 10, Pages: 333-338, ISSN: 0269-2139

JOURNAL ARTICLE

Srinivasan A, King RD, Muggleton SH, Sternberg MJEet al., 1997, Carcinogenesis predictions using inductive logic programming, 1st International Workshop on Intelligent Data Analysis in Medicine and Pharmacology (IDAMAP-96), at the 12th European Conference on Artificial Intelligence (ECAI-96), Publisher: KLUWER ACADEMIC PUBLISHERS, Pages: 243-260

CONFERENCE PAPER

Srinivasan A, King RD, Muggleton SH, Sternberg MJEet al., 1997, The Predictive Toxicology Evaluation challenge, 15th International Joint Conference on Artificial Intelligence, Publisher: MORGAN KAUFMANN PUB INC, Pages: 4-9, ISSN: 1045-0823

CONFERENCE PAPER

Srinivasan A, King RD, Muggleton SH, Sternberg MJEet al., 1997, Carcinogenesis predictions using ILP, Pages: 273-287, ISSN: 0302-9743

© Springer-Verlag Berlin Heidelberg 1997. Obtaining accurate structural alerts for the causes of chemical cancers is a problem of great scientific and humanitarian value. This paper follows up on earlier research that demonstrated the use of Inductive Logic Programming (ILP) for predictions for the related problem of mutagenic activity amongst nitroaromatic molecules. Here we are concerned with predicting carcinogenic activity in rodent bioassays using data from the U.S. National Toxicology Program conducted by the National Institute of Environmental Health Sciences. The 330 chemicals used here are significantly more diverse than the previous study, and form the basis for obtaining Structure-Activity Relationships (SARs) relating molecular structure to cancerous activity in rodents. We describe the use of the ILP system Progol to obtain SARs from this data. The rules obtained from Progol are comparable in accuracy to those from expert chemists, and more accurate than most state-of-the-art toxicity prediction methods. The rules can also be interpreted to give clues about the biological and chemical mechanisms of carcinogenesis, and make use of those learnt by Progol for mutagenesis. Finally, we present details of, and predictions for, an ongoing international blind trial aimed specifically at comparing prediction methods. This trial provides ILP algorithms an opportunity to participate at the leading-edge of scientific discovery.

CONFERENCE PAPER

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

Brutlag DL, Sternberg MJ, 1996, Sequences and topology challenges for algorithms and experts., Curr Opin Struct Biol, Vol: 6, Pages: 343-345, ISSN: 0959-440X

JOURNAL ARTICLE

Brutlag DL, Sternberg MJE, 1996, Sequences and topology - Challenges for algorithms and experts - Editorial overview, CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 6, Pages: 343-345, ISSN: 0959-440X

JOURNAL ARTICLE

Harrison PM, Sternberg MJE, 1996, The disulphide beta-cross: From cystine geometry and clustering to classification of small disulphide-rich protein folds, JOURNAL OF MOLECULAR BIOLOGY, Vol: 264, Pages: 603-623, ISSN: 0022-2836

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

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

King RD, Srinivasan A, Sternberg MJE, 1996, Relating chemical activity to structure: An examination of ILP successes, New Generation Computing, Vol: 14, ISSN: 0288-3635

JOURNAL ARTICLE

King RD, Sternberg MJE, 1996, Identification and application of the concepts important for accurate and reliable protein secondary structure prediction, PROTEIN SCIENCE, Vol: 5, Pages: 2298-2310, ISSN: 0961-8368

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

Srinivasan A, Muggleton SH, Sternberg MJE, King RDet al., 1996, Theories for mutagenicity: A study in first-order and feature-based induction, ARTIFICIAL INTELLIGENCE, Vol: 85, Pages: 277-299, ISSN: 0004-3702

JOURNAL ARTICLE

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