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SILCS specifications


Unique identifier OMICS_35318
Alternative name Site-Identification by Ligand Competitive Saturation
Stability Stable
Maintained Yes


No version available

SILCS citations


Computational methods in drug discovery

Beilstein J Org Chem
PMCID: 5238551
PMID: 28144341
DOI: 10.3762/bjoc.12.267

[…] ies and is available to download []. If two fragments bind to two non-overlapping nearby sites on a target protein, these fragments can be joined to obtain a possible new drug molecule. In the SILCS (site identification by ligand competitive saturation) method, molecular dynamics simulations are used to identify fragments that bind to a target [–]. SILCS uses explicit molecular dynamics simulation […]


Characterization of Mg2+ Distributions around RNA in Solution

PMCID: 5088455
PMID: 27819065
DOI: 10.1021/acsomega.6b00241

[…] which can be used to both evaluate the relative affinity of known Mg2+ binding sites and predict new ones. The GFE maps can be further discretized to identify Mg2+ binding sites using the so-called “Site-Identification by Ligand Competitive Saturation (SILCS) pharmacophore” method described elsewhere. Briefly, an energetic cutoff value, −3 kcal mol–1 in this study, is used as an upper limit to de […]


Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G Protein Coupled Receptors

J Chem Inf Model
PMCID: 4372819
PMID: 25692383
DOI: 10.1021/ci500729k

[…] known to be coupled to small conformational changes in their binding sites, accurate modeling of these sites is critical for future development of therapeutic agents for a wide range of diseases.,The site identification by ligand competitive saturation (SILCS) methodology is a fragment sampling technique that maps free energy affinity patterns of functional groups at protein surfaces, including LB […]


Parameter Choice Matters: Validating Probe Parameters for Use in Mixed Solvent Simulations

J Chem Inf Model
PMCID: 4144759
PMID: 25058662
DOI: 10.1021/ci400741u

[…] duce some of the experimental binding sites. Yang and Wang have conducted similar studies that included phenol with the alcohol/water mix to address aromatic interactions., Another MD-based approach, site identification by ligand competitive saturation (SILCS), was implemented with a ternary-solvent box composed of 1 M benzene (BNZ), 1 M propane, and water to locate hot spots and to reproduce expe […]


Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical like Monte Carlo Molecular Dynamics Simulations

J Chem Theory Comput
PMCID: 4053307
PMID: 24932136
DOI: 10.1021/ct500201y

[…] ion techniques have been employed in the past toward discovery or rational design of molecules that can bind to macromolecular targets with high affinity to achieve a desired biological outcome.− The Site Identification by Ligand Competitive Saturation (SILCS) method is one such technique that identifies the location and approximate affinities of different functional groups on a target macromolecu […]


The novel BH3 α helix mimetic JY 1 106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl xL and Mcl 1 protein–protein interactions with Bak

Mol Cancer
PMCID: 3663763
PMID: 23680104
DOI: 10.1186/1476-4598-12-42

[…] ANOVA: Analysis of variance; BH3: Bcl-2 homology domain 3; BH3: Bcl-2 homology domain 3; LGFE: Ligand Grid Free Energies; SILCS: Site identification by ligand competitive saturation; siRNA: Small interfering RNA; TUNEL: Terminal deoxynucleotidyl transferase dUTP nick end labeling; SD: Standard deviation. […]


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