Interactive Virtual Screening and Visualization Tools
This invention is a software plugin for PyMOL, named 'cluster_mols.py,' designed to accelerate the selection of chemical compounds from virtual screens. Its primary advantage lies in significantly reducing the time and effort required to identify promising compounds for experimental testing in drug discovery.
Description
The 'cluster_mols.py' software streamlines the compound selection process by introducing a hierarchical clustering approach. The workflow involves computing a similarity matrix from input compounds, performing hierarchical clustering, and then organizing these results into user-specified clusters. These clusters are then loaded into PyMOL with integrated visualization tools that highlight favorable and unfavorable polar contacts between the ligand and a specified protein, allowing for rapid assessment of compound compatibility. The software also introduces keyboard shortcuts and WASD movement for efficient navigation through the clusters, making the manual selection process extremely efficient. This method is unique in its emphasis on maximizing the utilization of expert knowledge and improving user interaction and visualization tools.Applications
- Pharmaceutical companies- Drug design and discovery companies
- Computational chemistry research
- Biotechnology firms and academic research institutions involved in lead optimization
Advantages
- Allows users to efficiently examine all compounds within a chemical scaffold and select the most desirable modifications.- Enables users to quickly disregard entire scaffolds that are not of interest, saving significant time.
- Applies visualization tools to highlight good and bad polar contacts, aiding in quick determination of compound-protein compatibility.
- Reduces the time-consuming and repetitive nature of manually cycling through individual compounds.
- Minimizes the risk of missing potentially useful compounds due to time constraints.