Proasis4 and Clustering of Binding Site Atoms

The reporting functionality of Proasis4 has been greatly extended with the addition of the new option of Clustering Binding Site Atoms.

For any set of overlaid structures in Proasis4, a comprehensive report is compiled that includes:

• overall similarity order for the set of binding sites
• structures grouped according to overall binding site similarity
• structures grouped according to ligand similarity
• residue labelling
• sequence variations
• residue flexibility according to RMSD about each protein atom, separately for mainchain and sidechain atoms
• atom-based cluster membership details, with separate reporting for mainchain and sidechain atoms

Two distinct clustering reports are created:

• a summary report that includes colour-coding of residues for each property, and
• a full report that provides detailed information for every binding site residue in each overlaid structure.

Reports can be created listing:

• only residues in close proximity to the ligand (more suited to chemists) and
• reports listing more distal residues (more interest to modellers/designers).

The new clustering report type provides a great deal of new information that was previously quite difficult to obtain, including details about binding site residue positions that are disordered or have distinct conformations.

This latest Proasis4 extension provides a powerful new analysis tool that contributes key insights about protein targets for structure based drug design.