Sequence-structure analysis and homology modeling and their application to formulate or test specific biological hypothesis remained a focus of the laboratory. Sequence-structure alignment is a key component of the homology modeling procedure. We generated a database of 1927 pairs of homologous proteins with known 3D structures and generated a Structural Alignment Database (SAD). This database was used to optimize parameters of sequence-structure alignments [Marsden 2004].
General informatics and data analysis is an integral part of computational genomics. Our previously developed MOID algorithm (Match Only Integral Distribution) for more accurate analysis of the expression data using high density oligonucleotide chips was compared and reviewed in [Zhou 2002]. We also developed the informatics environment for the mass-spectrometry/metabolobics project of Gary Siuzdak.