332 results found
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 BIOINFORMATICS, Pages: 47-54, ISSN: 0887-3585
Dokurno P, Bates PA, Band HA, et al., 1998, Crystal structure at 1.95 angstrom 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
Bates PA, Dokurno P, Freemont PS, et al., 1998, Conformational analysis of the first observed non-proline cis-peptide bond occurring within the complementarity determining region (CDR) of an antibody, JOURNAL OF MOLECULAR BIOLOGY, Vol: 284, Pages: 549-555, ISSN: 0022-2836
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, Morera 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
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
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
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
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
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
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
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
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.
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
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
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: 0302-9743
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
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
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
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
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
Oliva B, Bates PA, Querol E, et al., 1997, An automated classification of the structure of protein loops, JOURNAL OF MOLECULAR BIOLOGY, Vol: 266, Pages: 814-830, ISSN: 0022-2836
Srinivasan A, King RD, Muggleton SH, et 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
© 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.
Srinivasan A, King RD, Muggleton SH, et 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
Bates PA, Jackson RM, Sternberg MJE, 1997, Model building by comparison: A combination of expert knowledge and computer automation, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Pages: 59-67, ISSN: 0887-3585
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