molclaw-prolif-md

To compute ProLIF interaction fingerprints from an MD trajectory, provide topology inputs like .psf, .pdb, or .prmtop alongside trajectory files such as .dcd, .nc, or .xtc. The tool processes these inputs to generate standardized metrics and a detailed interaction frequency report.

Monitoring protein-ligand binding stability across simulation frames is achieved by calculating ProLIF interaction fingerprints to quantify contact frequencies. This approach evaluates whether a ligand maintains key contacts during a simulation to inform lead optimization.

Yes, you can analyze specific protein regions and ligand interactions during trajectory analysis by selecting target residues. The computation supports frame slicing and optional proximity-based interaction analysis to isolate specific binding contacts.

Yes, trajectory analysis for ProLIF fingerprints supports .xtc and .nc file formats, along with .dcd files. The required topology inputs can be provided as .psf, .pdb, or .prmtop files to successfully compute the interaction data.

Outputs from a ProLIF molecular dynamics trajectory analysis include status, messages, output files, frame counts, and a detailed interaction frequency report. These results summarize high-frequency interactions to help evaluate binding stability for lead optimization.