Department of Genetics, Stanford University Stanford, CA 94305-5120
Sacch3D, an extension of the Saccharomyces Genome Database project (SGD), presents in-depth structural information for every protein in the recently completed yeast genome. Links to SGD and other databases provide functional information about each protein. All yeast open reading frame peptide sequences (ORFs) are ranked according to the following criteria: (i) does the ORF have a known crystal structure? (ii) does it have any putative homologs with known structure? (iii) does it have any domains with known structure? (iv) can a three-dimensional (3D)structure be predicted?
Information is presented on the web with a user-friendly interface and multi-modal access including text, static images, interactive 3D viewing, and links to other relevant resources. As a first step, we have automatically generated and processed results of a BLASTP sequence comparision of all ORFs against all protein sequences in the PDB. Roughly 12 percent (730/6156) of yeast ORFs showed significant similarity to proteins of known structure. Of these, 64 percent (467) have been studied genetically. A given ORF is ranked according to its degree of similarity to a protein of known structure and information is provided about the biological role of this homolog. The structural data are presented as text, images, and interactive 3D models with a variety of 3D viewers (Java, RasMol, Cn3D, Kinemage, VRML). The figures and models are colorized automatically to indicate extent of sequence similarity with the yeast protein.
Although our initial method for assessing structure involved only sequence analysis, we hope to incorporate additional techniques for identifying structural homologs and predicting structures. In addition to colorizing a known structure to indicate regions of homology to a yeast protein, we intend to use homology modeling to generate a putative structure for the yeast protein. Furthermore, ORFs that show no significant sequence similarity to proteins of known structure are candidates for a threading analysis. Such predicted structures and their confidence levels will be clearly distinguished from actual structures.
An important goal of Sacch3D is to create a tool to automate the aquisition and presentation of structural information for all protein sequences in the yeast genome. We are also concerned with developing tools to enhance the usefulness of structural information which can work at different levels depending on the quality of the information available. We intend for Sacch3D to contribute to the effort to define the specifications for such tools which have general applications in genomic analysis.
Sacch3D is located at http://genome-www.stanford.edu/Sacch3D