Protein Database Provides 3-D Structures
StructureBank, developed by Cengent Therapeutics (www.cengent.com), is a scalable, relational database that stores protein sequences, 3-D coordinates, annotations, and other data.
"We took the sequence data from the human genome and converted it to 3-D structures, which can be adapted to in silico screening methods for developing compounds," explains Kal Ramnarayan, Ph.D., vp and CSO.
The database currently has protein models for 550 protein families (as defined by PROSITE) and more than 5,500 unique, proprietary structures. Average time from sequence to protein structure ranges from one week up to four weeks. This is much faster than crystallography, which can take up to six months, depending on the protein.
Instead of depending on the expertise of a computational chemist, says Dr. Ramnarayan, this database enables the user to look at sequence and structure data, and perform searches and comparisons across families of proteins.
Searches can be done using textual, sequential, or structural parameters. Proteins can be viewed as skeleton, ribbon, surface-view, or space-filled. Other customizable views include electrostatic potential, flexibility, amino acid type, strain energy, and others. Images can be magnified and rotated, and structures can be superposed or separated to highlight similarities and differences.
Protein information can be obtained from multiple sources including in-house research, public domain sources, and the company's proprietary database. In order to transfer data across disparate platforms in different fields, the company incorporated XML technology. This enables users to write just a few lines of code to read protein sequences or structure-based information for their own analysis.
"People now realize the total utility of protein structure information in drug discovery. Our platform will help people access protein structures readily if they have limited resources to access novel structure information by other experimental methodologies," says Dr. Ramnarayan.