Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design

  • Christina E. Faller
  • E. Prabhu Raman
  • Alexander D. MacKerellJr.
  • Olgun GuvenchEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1289)


Fragment-based drug design (FBDD) involves screening low molecular weight molecules (“fragments”) that correspond to functional groups found in larger drug-like molecules to determine their binding to target proteins or nucleic acids. Based on the principle of thermodynamic additivity, two fragments that bind nonoverlapping nearby sites on the target can be combined to yield a new molecule whose binding free energy is the sum of those of the fragments. Experimental FBDD approaches, like NMR and X-ray crystallography, have proven very useful but can be expensive in terms of time, materials, and labor. Accordingly, a variety of computational FBDD approaches have been developed that provide different levels of detail and accuracy.

The Site Identification by Ligand Competitive Saturation (SILCS) method of computational FBDD uses all-atom explicit-solvent molecular dynamics (MD) simulations to identify fragment binding. The target is “soaked” in an aqueous solution with multiple fragments having different identities. The resulting computational competition assay reveals what small molecule types are most likely to bind which regions of the target. From SILCS simulations, 3D probability maps of fragment binding called “FragMaps” can be produced. Based on the probabilities relative to bulk, SILCS FragMaps can be used to determine “Grid Free Energies (GFEs),” which provide per-atom contributions to fragment binding affinities. For essentially no additional computational overhead relative to the production of the FragMaps, GFEs can be used to compute Ligand Grid Free Energies (LGFEs) for arbitrarily complex molecules, and these LGFEs can be used to rank-order the molecules in accordance with binding affinities.

Key words

Fragment-based drug design (FBDD) Molecular dynamics (MD) Site identification by ligand competitive saturation (SILCS) Binding free energy FragMap Grid free energy (GFE) Ligand grid free energy (LGFE) 



NIH AI080968, CA107331, and R15GM099022; NSF XSEDE TG-MCB120007; Samuel Waxman Cancer Research Foundation; The University of Maryland Computer-Aided Drug Design Center; and University of New England start-up funds.

Conflict of interest: O.G. and A.D.M. are founders of SilcsBio LLC and are currently Manager and Chief Scientific Officer of the same, respectively.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Christina E. Faller
    • 1
  • E. Prabhu Raman
    • 2
  • Alexander D. MacKerellJr.
    • 2
  • Olgun Guvench
    • 1
    Email author
  1. 1.Department of Pharmaceutical Sciences, College of PharmacyUniversity of New EnglandPortlandUSA
  2. 2.Department of Pharmaceutical Sciences, School of PharmacyUniversity of MarylandBaltimoreUSA

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