SILCS

SILCS (Site Identification by Ligand Competitive Saturation) is a computational platform developed by Silcs Bio for structure-based drug discovery. It is designed for researchers working on ligand optimization, binding site analysis, and virtual screening against target proteins.

The platform uses FragMaps — three-dimensional maps derived from molecular simulation — to visualize and quantify ligand-protein interactions. An interactive demo is available that walks users through the capabilities of SILCS using a crystal structure of TrmD, a M1G37 tRNA methyltransferase (PDB ID 4YPX), as a reference example.

Core Capabilities

• Ligand optimization using FragMap-based interaction data
• Identification of ligand binding hotspots on a target protein
• Creation of 3D pharmacophore models for high-throughput screening
• Refinement and rescoring of docked ligand poses

SILCS FragMaps

• FragMaps provide rich, three-dimensional information about the binding site environment of a target protein
• They are used to guide decisions in ligand design and optimization workflows
• The interactive demo allows users to explore FragMap data at their own pace, with controls for zooming, rotating, and repositioning the molecular view

Interactive Demo Workflow

1. Load a starting protein structure (e.g., the crystal structure of TrmD)
2. Visualize FragMaps overlaid on the protein binding site
3. Step through a guided series of demonstrations illustrating how SILCS data informs ligand design decisions
4. Pause, zoom, and orient the 3D view at any point during the walkthrough

A live demo can be requested directly from Silcs Bio for a more in-depth walkthrough of the platform's capabilities in the context of specific research applications.