Internet On-Ramp Molecular Modeling on the Web

With the worldwide genomic sequencing efforts pro ducing a steady stream of data, the sequences of tens of thousands of proteins can now be determined. Un derstanding protein function requires knowledge of pro tein structure. Information on the 3-D structure of a pro tein can provide insight to the protein’s interactions with other molecules; this information can also be exploited in such endeavors as protein engineering, mutagene sis, and computer-aided drug design. Detailed structu r al information is available for only 10% of all known pro tein sequences. Of the remaining 90%, a homologous protein of known structure has been identified for 10%– 25%. For this subset, a rapid in silico approach to 3-D structure is accomplished using homology or compara tive modeling. For another 25% of the available protein sequences, structural models can be generated using secondary and tertiary structure prediction methods . Until recently, many biologists have been reluctant to use molecular modeling as a computational tool be cause of the high costs of modeling software, its use r “unfriendliness”, and the expensive hardware (usually UNIX ®platforms) dictated by the software. Biologists have thus been hindered from making critical associa tions relating biological structure to function. So, if you have a protein sequence (referred to as the query se quence) and would like to build a molecular model us ing Internet-based tools, here is a route map .