FTProd

FTProd analyzes solvent fragment-mapping and probe-docking results across multiple protein structures to identify and characterize druggable hot spots and binding-site variability.

Key Features:

• Multi-structure analysis: Facilitates simultaneous examination of multiple mutant structures and frames from molecular dynamics simulations to assess binding-site dynamics and variability.
• Fragment-based solvent mapping and probe docking: Leverages computational solvent fragment mapping and docks small molecular probes onto protein surfaces to map potential binding configurations.
• Clustering of probe binding poses: Clusters docked probe outputs to define recurrent binding configurations and identify conserved hot spots across structures.
• FTMAP integration: Compares and consolidates binding configurations generated by FTMAP for cross-structural analysis of fragment-mapping results.
• VMD extension: Operates as an extension for Visual Molecular Dynamics (VMD) to analyze structural ensembles and simulation frames.

Scientific Applications:

• Drug discovery: Identifies cross-structural druggable hot spots to guide design of small-molecule probes or therapeutics targeting conserved binding regions.
• Structural biology: Characterizes binding-site conservation and conformational variability across mutants and MD trajectories to inform functional and mechanistic studies.

Methodology:

Performs computational solvent fragment mapping and docks a series of small molecular probes onto protein surfaces, clusters the resulting probe binding poses, and compares FTMAP-generated configurations across multiple structures and simulation frames.