ProfessorMichaelSternberg

Janin J, Henrick K, Moult J, Ten Eyck L, Sternberg MJE, Vajda S, Vasker I, Wodak SJet al., 2003, CAPRI: A Critical Assessment of PRedicted Interactions, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Vol: 52, Pages: 2-9, ISSN: 0887-3585

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• Citations: 476

Smith GR, Sternberg MJE, 2003, Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Vol: 52, Pages: 74-79, ISSN: 0887-3585

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• Citations: 23

Sternberg MJE, Muggleton SH, 2003, Structure activity relationships (SAR) and pharmacophore discovery using Inductive Logic Programming (ILP), QSAR & COMBINATORIAL SCIENCE, Vol: 22, Pages: 527-532, ISSN: 1611-020X

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• Citations: 19

Alves R, Chaleil RAG, Sternberg MJE, 2002, Evolution of enzymes in metabolism: A network perspective (vol 320, pg 751, 2002), JOURNAL OF MOLECULAR BIOLOGY, Vol: 324, Pages: 387-387, ISSN: 0022-2836

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Müller A, MacCallum RM, Sternberg MJE, 2002, Structural characterization of the human proteome, GENOME RESEARCH, Vol: 12, Pages: 1625-1641, ISSN: 1088-9051

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• Citations: 57

Alves R, Chaleil RAG, Sternberg MJE, 2002, Evolution of enzymes in metabolism: A network perspective, JOURNAL OF MOLECULAR BIOLOGY, Vol: 320, Pages: 751-770, ISSN: 0022-2836

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• Citations: 62

Vajda S, Vakser IA, Sternberg MJE, Janin Jet al., 2002, Modeling of protein interactions in genomes, Proteins: Structure, Function, and Genetics, Vol: 47, Pages: 444-446, ISSN: 0887-3585

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Vajda S, Vakser IA, Sternberg MJE, Janin Jet al., 2002, Modeling of protein interactions in genomes., Proteins, Vol: 47, Pages: 444-446

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Smith GR, Sternberg MJE, 2002, Prediction of protein-protein interactions by docking methods, CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 12, Pages: 28-35, ISSN: 0959-440X

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• Citations: 356

Alves R, Chaleil RAG, Sternberg MJE, 2002, Erratum: Evolution of enzymes in metabolism: A network perspective (Journal of Molecular Biology (2002) 320 (751-770)), Journal of Molecular Biology, Vol: 324, ISSN: 0022-2836

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Sternberg MJE, Alves R, Chaleil R, Kelley LA, Islam SA, MacCallum RM, Muller Aet al., 2002, EXPLOITING PROTEIN STRUCTURE IN THE POST GENOME ERA, Publisher: INT UNION CRYSTALLOGRAPHY, Pages: C4-C4, ISSN: 2053-2733

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Stapley BJ, Kelley LA, Sternberg MJE, 2002, Predicting the sub-cellular location of proteins from text using support vector machines., Pac Symp Biocomput, Pages: 374-385, ISSN: 2335-6928

We present an automatic method to classify the sub-cellular location of proteins based on the text of relevant medline abstracts. For each protein, a vector of terms is generated from medline abstracts in which the protein/gene's name or synonym occurs. A Support Vector Machine (SVM) is used to automatically partition the term space and to thus discriminate the textual features that define sub-cellular location. The method is benchmarked on a set of proteins of known sub-cellular location from S. cerevisiae. No prior knowledge of the problem domain nor any natural language processing is used at any stage. The method out-performs support vector machines trained on amino acid composition and has comparable performance to rule-based text classifiers. Combining text with protein amino-acid composition improves recall for some sub-cellular locations. We discuss the generality of the method and its potential application to a variety of biological classification problems.

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Turcotte M, Muggleton SH, Sternberg MJE, 2001, Generating protein three-dimensional fold signatures using inductive logic programming, COMPUTERS & CHEMISTRY, Vol: 26, Pages: 57-64, ISSN: 0097-8485

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• Citations: 4

Shiels C, Islam SA, Vatcheva R, Sasieni P, Sternberg MJE, Freemont PS, Sheer Det al., 2001, PML bodies associate specifically with the MHC gene cluster in interphase nuclei, Journal of Cell Science, Vol: 114, Pages: 3705-3716, ISSN: 0021-9533

Promyelocytic leukemia (PML) bodies are nuclear multiprotein domains. The observations that viruses transcribe their genomes adjacent to PML bodies and that nascent RNA accumulates at their periphery suggest that PML bodies function in transcription. We have used immuno-FISH in primary human fibroblasts to determine the 3D spatial organisation of gene-rich and gene-poor chromosomal regions relative to PML bodies. We find a highly non-random association of the gene-rich major histocompatibility complex (MHC) on chromosome 6 with PML bodies. This association is specific for the centromeric end of the MHC and extends over a genomic region of at least 1.6 megabases. We also show that PML association is maintained when a subsection of this region is integrated into another chromosomal location. This is the first demonstration that PML bodies have specific chromosomal associations and supports a model for PML bodies as part of a functional nuclear compartment.

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• Citations: 105

Saqi MAS, Sternberg MJE, 2001, A structural census of metabolic networks for <i>E</i>. <i>coli</i>, JOURNAL OF MOLECULAR BIOLOGY, Vol: 313, Pages: 1195-1206, ISSN: 0022-2836

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• Citations: 13

Shiels C, Islam SA, Vatcheva R, Sasieni P, Sternberg MJE, Freemont PS, Sheer Det al., 2001, PML bodies associate specifically with the MHC gene cluster in interphase nuclei, JOURNAL OF CELL SCIENCE, Vol: 114, Pages: 3705-3716, ISSN: 0021-9533

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• Citations: 102

Aloy P, Querol E, Aviles FX, Sternberg MJEet al., 2001, Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking, JOURNAL OF MOLECULAR BIOLOGY, Vol: 311, Pages: 395-408, ISSN: 0022-2836

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• Citations: 201

Turcotte M, Muggleton SH, Sternberg MJE, 2001, The effect of relational background knowledge on learning of protein three-dimensional fold signatures, 8th International Conference on Inductive Logic Programming (ILP98), Publisher: SPRINGER, Pages: 81-95, ISSN: 0885-6125

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• Citations: 14

Jennings AJ, Edge CM, Sternberg MJE, 2001, An approach to improving multiple alignments of protein sequences using predicted secondary structure, PROTEIN ENGINEERING, Vol: 14, Pages: 227-231, ISSN: 0269-2139

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• Citations: 19

Turcotte M, Muggleton SH, Sternberg MJE, 2001, Automated discovery of structural signatures of protein fold and function, JOURNAL OF MOLECULAR BIOLOGY, Vol: 306, Pages: 591-605, ISSN: 0022-2836

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• Citations: 24

Bates PA, Kelley LA, MacCallum RM, Sternberg MJEet al., 2001, Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Pages: 39-46, ISSN: 0887-3585

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• Citations: 456

Huyton T, Bates PA, Zhang XD, Sternberg MJE, Freemont PSet al., 2000, The BRCA1 C-terminal domain: structure and function, MUTATION RESEARCH-DNA REPAIR, Vol: 460, Pages: 319-332, ISSN: 0921-8777

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• Citations: 126

Kelley LA, MacCallum RM, Sternberg MJE, 2000, Enhanced genome annotation using structural profiles in the program 3D-PSSM, JOURNAL OF MOLECULAR BIOLOGY, Vol: 299, Pages: 499-520, ISSN: 0022-2836

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• Citations: 1299

Kelley LA, MacCallum RM, Sternberg MJE, 2000, Enhanced genome annotation using structural profiles in the program 3D-PSSM, Journal of Molecular Biology, Vol: 299, Pages: 501-522, ISSN: 0022-2836

A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18%. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95% confidence. 3D-PSSM is available to the community as a web server: http://www.bmm.icnet.uk/servers/3dpssm. (C) 2000 Academic Press.

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• Citations: 1126

MacCallum RM, Kelley LA, Sternberg MJE, 2000, SAWTED: Structure Assignment With Text Description - Enhanced detection, of remote homologues with automated SWISS-PROT annotation comparisons, BIOINFORMATICS, Vol: 16, Pages: 125-129, ISSN: 1367-4803

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• Citations: 48

Sternberg MJ, Gabb HA, Jackson RM, Moont Get al., 2000, Protein-protein docking. Generation and filtering of complexes., Methods Mol Biol, Vol: 143, Pages: 399-415, ISSN: 1064-3745

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Müller A, MacCallum RM, Sternberg MJE, 1999, Benchmarking PSI-BLAST in genome annotation, JOURNAL OF MOLECULAR BIOLOGY, Vol: 293, Pages: 1257-1271, ISSN: 0022-2836

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• Citations: 88

Sternberg MJE, Bates PA, Kelley LA, MacCallum RMet al., 1999, Prepress in protein structure prediction: assessment of CASP3, CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 9, Pages: 368-373, ISSN: 0959-440X

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• Citations: 87

Moont G, Gabb HA, Sternberg MJE, 1999, Use of pair potentials across protein interfaces in screening predicted docked complexes, Proteins: Structure, Function and Genetics, Vol: 35, Pages: 364-373, ISSN: 0887-3585

Empirical residue-residue pair potentials are used to screen possible complexes for protein-protein dockings. A correct docking is defined as a complex with not more than 2.5 Å root-mean-square distance from the known experimental structure. The complexes were generated by 'ftdock' (Gabb et al. J Mol Biol 1997;272:106-120) that ranks using shape complementarity. The complexes studied were 5 enzyme-inhibitors and 2 antibody-antigens, starting from the unbound crystallographic coordinates, with a further 2 antibody- antigens where the antibody was from the bound crystallographic complex. The pair potential functions tested were derived both from observed intramolecular pairings in a database of nonhomologous protein domains, and from observed intermolecular pairings across the interfaces in sets of nonhomologous heterodimers and homodimers. Out of various alternate strategies, we found the optimal method used a mole-fraction calculated random model from the intramolecular pairings. For all the systems, a correct docking was placed within the top 12% of the pair potential score ranked complexes. A combined strategy was developed that incorporated 'multidock,' a side-chain refinement algorithm (Jackson et al. J Mol Biol 1998;276:265- 285). This placed a correct docking within the top 5 complexes for enzyme- inhibitor systems, and within the top 40 complexes for antibody-antigen systems.

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• Citations: 239

Moont G, Gabb HA, Sternberg MJE, 1999, Use of pair potentials across protein interfaces in screening predicted docked complexes, PROTEINS-STRUCTURE FUNCTION AND GENETICS, Vol: 35, Pages: 364-373, ISSN: 0887-3585

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• Citations: 224