• 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 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.


Single Step Free Energy Perturbation: After running an SSFEP simulation of a ligand-protein complex, predicting the direction of binding free energy change for isosteres of that ligand– -H to CH3, -H to -Cl, -H to -Fl, etc. — takes just minutes.

Our Team

Ken Malone
Chief Executive Officer
Ken Malone provides leadership and business operations expertise. He has engaged in the commercialization of hundreds of new products, and brings a broad experience base from 25 years in business operations, marketing, intellectual property management, M&A, finance and government affairs.
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.
Alexander MacKerell
Chief Scientific Officer
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.
Tina Guvench
Technical Marketing Manager
Tina Guvench provides sales and marketing management. She has a Master’s of Science in Chemistry from the University of Washington- Seattle, and a Bachelor’s of Science in Biochemistry from the University of New England. She brings a broad scientific and technical background to meet customer needs.
Sunhwan Jo
Commercial Development Director
Dr. Sunhwan Jo provides expertise in computational modeling and simulation software development. Jo has a passion for developing user-friendly software for the scientific community.

Get in touch

Contact us to learn more