Design, development and analysis of bioinformatics and chemoinformatics databases

Databases play important roles in the day-to-clay research activities in Bioinformatics and Chemoinformatics. Although large databases such as the Protein Data Bank and Genbank provide comprehensive collections of data, small Bioinformatics databases that focus on specialized areas, integrate data from various sources and present value-added features often give users easier access and better results. Many commercial databases of chemicals have long been available, but the concept of large-scale public databases of molecules with efficient Web-based searching capabilities is still relatively new. We describe the design and statistical analysis of the Interchain β-sheets (ICBS) Database. We have created a comprehensive database of ICBS interactions and derived the ICBS index to quantify the relative contributions of the β-ladders in the overall interaction. First- and second-order statistics are computed regarding amino acid composition and pairing at different positions in the β-strands. Analysis of the database reveals a 15.8% prevalence of significant ICBS interactions. A full range of non-covalent interactions between side chains complement the hydrogen-bonding interactions between the main chains. Polar amino acids pair preferentially with polar amino acids and non-polar amino acids pair preferentially with non-polar amino acids among antiparallel (i; j) pairs. We present the ChemDB database, a public database of small molecules and related chemoinformatics resources. The current version of the database contains approximately 4.1 million commercially available compounds and 8.2 million counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, and unique search functions such as similarity search and name search, etc. Large-scale computational analysis of pre-mRNA splicing data is still in its infancy. We use the EST-based alternative splicing database to compute, the probability of splicing events based on the architecture of exons and introns. Our studies show that the size and location of the flanking introns control the mechanism of splice-site recognition and influence the frequency and type of alternative splicing. We have examined a specific type of alternative splicing and found that the spliceosome is more prone to violate splicing fidelity at the second step of catalysis.