CCG announces new version of protein structure database and visualization system

Chemical Computing Group (CCG) today announces a new version of its structure database and visualization system, PSILO, featuring new analytical tools and enhanced search capabilities. PSILO is an integrated repository for public and in-house structural data that allows easy collaboration and data sharing across organizational departments. Using a standard web browser interface, PSILO's structural data can be searched, visualized, registered, annotated and tracked. The new and enhanced features in PSILO 2011.09 include:

3D query statistical analysis tools

• Ligand-independent pocket similarity searches
• Export protein families to common reference frame
• Metal ion treatment as ligands

"The new additions demonstrate our ongoing commitment to lead the structural repository and visualization market," commented Paul Labute, president and CEO of CCG. PSILO 2011.09 incorporates an automatic process for ligand-independent pocket detection, thereby expanding the space of the searchable pocket database. Paul Labute explained, "We eliminated previous pocket search constraints by implementing a pocket detection algorithm, thus providing richer query results. With a greater pool of potential binding sites, researchers are now in a better position, for example, to identify potential drug side effects or new therapeutic areas."

PSILO has a simple yet powerful Google-like search bar in which multiple search criteria, such as combinations of text, sequence, 2D substructure and 3D geometry specifications, can be expressed. In PSILO 2011.09, new statistical analysis tools are available to investigate the significance of defined 3D geometric constraints within PDB and in-house structural data. Paul Labute said, "The ability to understand the statistical relevance of protein-ligand or protein-protein interaction motifs using scatter plots, histograms, or sorting by constraint values will allow researchers to make more informed decisions about critical interactions and to facilitate drug design."

In this new version of PSILO, metal ions are treated as ligands making it possible to visualize ligand interaction diagrams for metals and to perform 3D/2D metal ion searches. Non-standard amino acids can also be searched. Another addition to PSILO 2011.09 is the ability to choose a family reference frame when exporting hit lists. This ability to select reference orientations allows scientists to easily compare project structures, helping identify relevant interactions to be considered in drug development.

Source: Chemical Computing Group