Publications
368 results found
Betts MJ, Sternberg MJE, 1999, An analysis of conformational changes on protein-protein association: implications for predictive docking, PROTEIN ENGINEERING, Vol: 12, Pages: 271-283, ISSN: 0269-2139
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- Citations: 173
Kelley LA, MacCallum RM, Sternberg MJE, 1999, Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM, Pages: 218-225
A method (3D-PSSM) to recognize remote protein sequence homologues is described. The method uses homologous proteins of similar three-dimensional structure in the SCOP database to obtain a structural equivalence of residues. These equivalences are used to extend multiply-aligned sequences obtained by standard sequence searches (i.e. 1D-profiles). The resultant 3D profile is converted into a position specific scoring matrix (a 3D-PSSM). The approach is benchmarked on recognizing remote homologues in the SCOP database and comparing the hit and error rates. 3D-PSSMs are compared with 1D-PSSMs and with two widely-used sensitive search approaches - PSI-BLAST and global dynamic programming using the BLOSUM62 matrix. In a cross-validated benchmark, 3D-PSSMs and 1D-PSSMs achieved similar results and both have lower error rates compared to the other two methods when recognizing remote homologues. The combination of 1D- and 3D-PSSMs provide improved performance over either individual method and thus can identify remote homologies that would not be detected by PSI-BLAST. It is envisaged that 3D-PSSM can complement current homology searches in a two-stage approach in which 3D-PSSMs will follow an initial search using PSI-BLAST or dynamic programming.
Bates PA, Sternberg MJE, 1999, Model building by comparison at CASP3: Using expert knowledge and computer automation, Proteins: Structure, Function and Genetics, Vol: 37, Pages: 47-54, ISSN: 0887-3585
Ten models were constructed for the comparative modeling section of the Critical Assessment of Techniques for Protein Structure Prediction-3 (CASP3). Sequence identity between each target and the best possible parent(s) ranged between 12% and 64%. The modeling protocol is a mixture of automated computer algorithms with human intervention at certain critical stages. In particular, intervention is required to check sequence alignments and the selection of parameters for various computer programs. Seven of the targets were constructed from single-parent templates, and three were constructed from multiple parents. The reasons for such a high ratio of modeling from single parents only are discussed. Models constructed from multiple parents were found to be more accurate than models constructed from single parents only. A novel loop-modeling algorithm is presented that consists of fragment database searches, several fragment libraries, and mean-field calculations on representative fragment candidates.
Fischer D, Barret C, Bryson K, et al., 1999, CAFASP-1: Critical assessment of fully automated structure prediction methods, Proteins: Structure, Function and Genetics, Vol: 37, Pages: 209-217, ISSN: 0887-3585
The results of the first Critical Assessment of Fully Automated Structure Prediction (CAFASP-1) are presented. The objective was to evaluate the success rates of fully automatic web servers for fold recognition which are available to the community. This study was based on the targets used in the third meeting on the Critical-Assessment of Techniques for Protein Structure Prediction (CASP-3). However, unlike CASP-3, the study was not a blind trial, as it was held after the structures of the targets were known. The aim was to assess the performance of methods without the user intervention that several groups used in their CASP-3 submissions. Although it is clear that 'human plus machine' predictions are superior to automated ones, this CAFASP-1 experiment is extremely valuable for users of our methods; it provides an indication of the performance of the methods alone, and not of the 'human plus machine' performance assessed in CASP. This information may aid users in choosing which programs they wish to use and in evaluating the reliability of the programs when applied to their specific prediction targets. In addition, evaluation of fully automated methods is particularly important to assess their applicability at genomic scales. For each target, groups submitted the top-ranking folds generated from their servers. In CAFASP-1 we concentrated on fold-recognition web servers only and evaluated only recognition of the correct fold, and not, as in CASP-3, alignment accuracy. Although some performance differences appeared within each of the four target categories used here, overall, no single server has proved markedly superior to the others. The results showed that current fully automated fold recognition servers can often identify remote similarities when pairwise sequence search methods fall. Nevertheless, in only a few cases outside the family-level targets has the score of the top-ranking fold been significant enough to allow for a confident fully automated prediction.
Bates PA, Sternberg MJE, 1999, Model building by comparison at CASP3: Using expert knowledge and computer automation, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Pages: 47-54, ISSN: 0887-3585
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- Citations: 127
Zhang X, Morera S, Bates PA, et al., 1999, STRUCTURE OF AN XRCC1 BRCT DOMAIN: A NEW PROTEIN PROTEIN INTERACTION MODULE., Publisher: INT UNION CRYSTALLOGRAPHY, Pages: 292-292, ISSN: 2053-2733
Fischer D, Barret C, Bryson K, et al., 1999, CAFASP-1: Critical assessment of fully automated structure prediction methods, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Pages: 209-217, ISSN: 0887-3585
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- Citations: 145
Dokurno P, Bates PA, Band HA, et al., 1998, Crystal structure at 1.95 Å resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition, JOURNAL OF MOLECULAR BIOLOGY, Vol: 284, Pages: 713-728, ISSN: 0022-2836
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- Citations: 64
Bates PA, Dokurno P, Freemont PS, et al., 1998, Conformational analysis of the first observed non-proline <i>cis</i>-peptide bond occurring within the complementarity determining region (CDR) of an antibody, JOURNAL OF MOLECULAR BIOLOGY, Vol: 284, Pages: 549-555, ISSN: 0022-2836
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- Citations: 22
Aloy P, Moont G, Gabb HA, et al., 1998, Modelling repressor proteins docking to DNA, PROTEINS-STRUCTURE FUNCTION AND GENETICS, Vol: 33, Pages: 535-549, ISSN: 0887-3585
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- Citations: 44
Aloy P, Moont G, Gabb HA, et al., 1998, Modelling repressor proteins docking to DNA, Proteins: Structure, Function, and Genetics, Vol: 33, Pages: 535-549, ISSN: 0887-3585
Aloy P, Moont G, Gabb HA, et al., 1998, Modelling repressor proteins docking to DNA, Proteins: Structure, Function and Genetics, Vol: 33, Pages: 535-549, ISSN: 0887-3585
The docking of repressor proteins to DNA starting from the unbound protein and model-built DNA coordinates is modeled computationally. The approach was evaluated on eight repressor/DNA complexes that employed different modes for protein/DNA recognition. The global search is based on a protein-protein docking algorithm that evaluates shape and electrostatic complementarity, which was modified to consider the importance of electrostatic features in DNA-protein recognition. Complexes were then ranked by an empirical score for the observed amino acid/nucleotide pairings (i.e., protein-DNA pair potentials) derived from a database of 20 protein/DNA complexes. A good prediction had at least 65% of the correct contacts modeled. This approach was able to identify a good solution at rank four or better for three out of the eight complexes. Predicted complexes were filtered by a distance constraint based on experimental data defining the DNA footprint. This improved coverage to four out of eight complexes having a good model at rank four or better. The additional use of amino acid mutagenesis and phylogenetic data defining residues on the repressor resulted in between 2 and 27 models that would have to be examined to find a good solution for seven of the eight test systems. This study shows that starting with unbound coordinates one can predict three-dimensional models for protein/DNA complexes that do not involve gross conformational changes on association.
Zhang XD, Moréra S, Bates PA, et al., 1998, Structure of an XRCC1 BRCT domain:: a new protein-protein interaction module, EMBO JOURNAL, Vol: 17, Pages: 6404-6411, ISSN: 0261-4189
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- Citations: 208
Islam SA, Carvin D, Sternberg MJE, et al., 1998, HAD, a data bank of heavy-atom binding sites in protein crystals: a resource for use in multiple isomorphous replacement and anomalous scattering, ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, Vol: 54, Pages: 1199-1206, ISSN: 0907-4449
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- Citations: 24
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
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- Citations: 180
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
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- Citations: 15
Oliva B, Bates PA, Querol E, et 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
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- Citations: 65
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
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- Citations: 96
Jackson RM, Gabb HA, Sternberg MJE, 1998, Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem, JOURNAL OF MOLECULAR BIOLOGY, Vol: 276, Pages: 265-285, ISSN: 0022-2836
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- Citations: 208
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
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.
Russell RB, Saqi MAS, Bates PA, et 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
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- Citations: 55
Muggleton S, Srinivasan A, King RD, et 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: 2945-9133
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- Citations: 8
Luo JC, Islam SA, Russell RB, et al., 1998, A world-wide web server of protein domain assignment, 4th Chinese Peptide Symposium (CPS-96), Publisher: SPRINGER, Pages: 235-236
King RD, Sternberg MJE, Muggleton SH, et al., 1998, Recent developments in applying machine learning to drug design, Conference of the NATO Advanced Study Institute on Experimental and Computational Approaches to Structure-Based Drug Design, Publisher: SPRINGER, Pages: 151-162, ISSN: 0168-132X
Sternberg MJ, Aloy P, Gabb HA, et 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.
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
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- Citations: 651
King RD, Saqi M, Sayle R, et al., 1997, DSC: public domain protein secondary structure prediction, COMPUTER APPLICATIONS IN THE BIOSCIENCES, Vol: 13, Pages: 473-474, ISSN: 0266-7061
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- Citations: 54
Russell RB, Saqi MAS, Sayle RA, et 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
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- Citations: 167
Lohmeyer M, Harrison PM, Kannan S, et 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
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- Citations: 26
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
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- Citations: 24
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