Comprehensive structural classification of ligand binding motifs in proteins

Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and universality of ligand binding sites in protein structures, we conducted the all-against-all atomic-level structural comparison of over 180,000 ligand binding sites found in all the known structures in the Protein Data Bank by using a recently developed database search and alignment algorithm. By applying a hybrid top-down-bottom-up clustering analysis to the comparison results, we determined approximately 3000 well-defined structural motifs of ligand binding sites. Apart from a handful of exceptions, most structural motifs were found to be confined within single families or superfamilies, and to be associated with particular ligands. Furthermore, we analyzed the components of the similarity network and enumerated more than 4000 pairs of ligand binding sites that were shared across different protein folds.Comment: 13 pages, 8 figure

NCeSS Project : Data mining for social scientists

We will discuss the work being undertaken on the NCeSS data mining project, a one year project at the University of Manchester which began at the start of 2007, to develop data mining tools of value to the social science community. Our primary goal is to produce a suite of data mining codes, supported by a web interface, to allow social scientists to mine their datasets in a straightforward way and hence, gain new insights into their data. In order to fully define the requirements, we are looking at a range of typical datasets to find out what forms they take and the applications and algorithms that will be required. In this paper, we will describe a number of these datasets and will discuss how easily data mining techniques can be used to extract information from the data that would either not be possible or would be too time consuming by more standard methods

One Homonym per Translation

The study of homonymy is vital to resolving fundamental problems in lexical semantics. In this paper, we propose four hypotheses that characterize the unique behavior of homonyms in the context of translations, discourses, collocations, and sense clusters. We present a new annotated homonym resource that allows us to test our hypotheses on existing WSD resources. The results of the experiments provide strong empirical evidence for the hypotheses. This study represents a step towards a computational method for distinguishing between homonymy and polysemy, and constructing a definitive inventory of coarse-grained senses.Comment: 8 pages, including reference

Clustering aspects and the shell model

In this talk I shall discuss the clustering aspect and the shell model. I shall first discuss the $\alpha$-cluster aspects based on the shell model calculations. Then I shall discuss the spin zero ground state dominance in the presence of random interactions and a new type of cluster structure for fermions in a single-$j$ shell in the presence of only pairing interaction with the largest multiplicity.Comment: 10 pages and 3 figures. International symposium in Nara, to appear in Nuclear Physics