New Peer Reviewed Article Demonstrates SilcsBio, LLC’s Performance

New Peer Reviewed Article Demonstrates SilcsBio, LLC’s Performance

Baltimore, Maryland, 4 November 2016

Recently published research has found that SilcsBio’s product, single-step free energy perturbation (SSFEP), demonstrated equal or more accurate results than standard free energy perturbation (FEP) but a thousand times faster. Additionally, SilcsBio’s site-identification by ligand competitive saturation (SILCS) product yielded relative free energies most consistent with experimental results.

“Computer-Aided Drug Design efforts often seek to compare ligand modifications as a means of predicting gains in binding affinity and guiding experimental work. However, due to a large computational burden, methods like FEP are not suited to evaluation of large sets of ligand modifications.” said Dr. Kaushik Lakkaraju, Director of Product Development at SilcsBio.

The study undertaken by researchers at Pfizer, Inc. and University of Maryland, Baltimore appears in the Journal of Computational Chemistry entitled “Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by ligand competitive saturation approaches.”

The authors compare FEP with two SilcsBio technologies, SILCS and SSFEP, to estimate relative binding free energies of ligand-protein complexes for proteins ACK1 and p38 MAP kinase. SILCS maps chemical functional group interactions with target proteins to give quantitative insights to drive ligand optimization. SSFEP uses a ligand scanning approach to evaluate single-atom and small functional group modifications to the ligand.

The SilcsBio methods employ a computationally-intensive pre-computation step that allows for more computationally efficient subsequent calculations compared to FEP. Notably, SILCS’ ligand grid free energy (LGFE) method yielded relative free energies most consistent with experimental results in the systems studied.

About SilcsBio, LLC: SilcsBio started operations in April 2013 based on licensed intellectual property developed by Dr. Alexander D. MacKerell, Jr at the University of Maryland, Baltimore where he is the Grollman-Glick Professor of Pharmaceutical Sciences and Director of the Computer-Aided Drug Design Center. The company is headquartered at Spark-Baltimore located at 8 Market Place, Suite 300, Baltimore, MD 21202.


For more information, please contact: Tina Guvench,, 410.645.0387

Find the full article here: E. Prabhu Raman, S. Kaushik Lakkaraju, R. Aldrin Denny, A. D. MacKerell, Jr. J. Comput. Chem. 2016, DOI: 10.1002/jcc.24522.