• bcl6

    SILCS detects hot-spots on the entire surface of the protein (Guvench et al., PLOS Comput. Bio.)

  • cryptic

    SILCS identifies cryptic pockets in protein-protein interfaces (Foster et al., J. Comput. Chem.)

  • trypsin

    SILCS and the S1 pocket in trypsin (Raman et al., J. Chem. Inf. Model.)

  • singlestep

    Affinity changes from chemical modifications are computed in seconds (Raman et al., J. Chem. Theory Comput.)

What we do

Free Energy Based Ligand Design

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.



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 fragment-based drug design. 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.

Our Team

Ken Malone
Chief Executive Officer
Ken Malone provides strategic planning and general business management. Malone has built his career on creating economic value from science. Whether it was developing new business lines for global corporations or spinning out new ventures from universities, he has engaged in the commercialization of hundreds of new products.
Kelli Booth
Chief Operating Officer
Kelli Booth provides sales, marketing and project management. Booth has a proven track record of bringing new products to market. Whether it was a company developing new fiber intellectual property that generated positive cash flow or developing advanced materials for the defense industry, she fills the role of energetic dealmaker.
Olgun Guvench
Managing Partner
Dr. Olgun Guvench provides product development and represents the corporation’s partners. Guvench has 15 years of experience in computational chemistry.
Alexander Mackerell
Chief Scientist
Dr. Alex MacKerell provides intellectual property and a deep understanding of the market’s technology. MacKerell is the Grollman-Glick Professor of Pharmaceutical Sciences and Director, Computer-Aided Design Center at the University of Maryland.