A collaborative project with the Laboratory of Experimental and Computational Biology, NCI is underway to develop a new version of the GOR method. This new version uses the profile of homologue proteins to a query sequence detected by the PSIBLAST program. At present the method is predicting correctly 74.1% of helix, extended and aperiodic residues after crossvalidation for a database of 513 amino acid sequences. Protein secondary structure prediction represents an important element of the protein classification and will be a component to the understanding of the mechanism of protein folding. Methods have been developed in our laboratory to predict the tertiary structure from the predicted secondary structure (FORESST). Virtually all functional predictions based on structure similarities rely at least in part on the prediction of the secondary structures. Thus it is clearly important to search for better accuracy in their prediction. In a second project with the Hormone Action and Oncogenensis Section, NCI, we provided a model and analysis paradigm for confocal fluorescence microscopy images of cell nuclei in metaphase and interphase. This proceedure selectively labels specific chromosomes, and is being used to determine the underlying organization of chromosomes within the nuclei, with a view to chromosome translocation, in normal and cancer cells. Our approach uses geometric statistics to determine if the apparent preferential location of certain pairs and triples of chromosomes is in fact statistically significant. ABS staff also provided advice and collaboration in areas of statistical analysis, ligand binding data analysis, dose-response curve analysis, repeated-measures ANOVA and MANOVA. The ABS also maintains a specialized library of software, available for download to the scientific community. Recently, new versions of P-SCAN and F-SCAN were made available in this manner and have been accesses by numerous laboratories around the country and around the globe. The ABS web server also provides a number of unique sequence analysis services, including secondary structure prediction by the GOR4 algorithm, multiple sequence alignment by CLUSTALW, and various reformatting services.
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