If you want to perform simulations on a system that contains a small organic molecule using the CHARMM force field, you’ve come to the right place. The CGenFF program will provide you with the most comprehensive parameters for your specific molecule, which you can read into your simulation software together with the main CGenFF topology and parameter files and any combination of CHARMM biomolecular force field files.
SILCS is computational chemical functional group mapping. SILCS is distinguished from competing methods by: rigorous free energies for any ligand in any pose computed in seconds after a preconditioning step with full target flexibility, explicit molecular solvation, an infinite palette of fragments, and results at experimental temperatures and pressures.
SSFEP stands for Single Step Free Energy Perturbation. After running a SILCS simulation using a particular set of fragments or a simulation of a ligand-protein complex, getting results for isosteres of those fragments — -H to CH3, -H to -Cl, -H to -Fl, etc. — takes just minutes. And the results are true free energies.
What we do
SilcsBio provides software and services for unlocking the full potential of computer driven drug design. Our algorithms for mapping proteins will provide you with a level of detail you have never before experienced. From our highly accurate free energy maps to conformational nuances revealing hidden pockets of opportunity, you will discover a whole new world of possibilities.