Enhanced mixed solvent MD
Site-Identification by Ligand Competitive Saturation (SILCS) generates 3-D maps (FragMaps) of interaction patterns for chemical functional groups with your target molecule. SILCS accounts for intricacies of protein dynamics, providing tools to optimize ligand scaffolds using qualitative and quantitative binding pocket insights, allowing more rapid and effective drug design.
Innovative Small Molecule Drug design with the SILCS toolset
SILCS uses multiple small molecule probes with various functional groups, explicit solvent modeling, and target molecule flexibility to perform protein target mapping. A Grand Canonical Monte Carlo approach drives probe sampling beyond the limits of diffusion and makes SILCS particularly useful for probing cryptic/transient binding pockets.
SILCS Applied to GPCRs
In this GPCR SILCS correctly predicts functional group affinities of a known ligand while offering optimization solutions for this ligand. In addition SILCS has identified novel agonists and a novel allosteric site and allosteric modulators for the beta2-adrenertic receptor.
P38 MAP Kinase FragMaps
FragMaps of P38 MAP Kinase with ligand overlaid on the FragMaps. FragMaps colored by fragment type: green = apolar, red = H-bond acceptor, blue = H-bond donor, orange = negative, and cyan = positive charge. FragMap densities near the bound inhibitor provide options for ligand optimization.
SILCS Applied to GPCRs
In this GPCR SILCS correctly predicts functional group affinities of a known ligand while offering optimization solutions for this ligand. In addition SILCS has identified novel agonists and a novel allosteric site and allosteric modulators for the beta2-adrenertic receptor.
P38 MAP Kinase FragMaps
FragMaps of P38 MAP Kinase with ligand overlaid on the FragMaps. FragMaps colored by fragment type: green = apolar, red = H-bond acceptor, blue = H-bond donor, orange = negative, and cyan = positive charge. FragMap densities near the bound inhibitor provide options for ligand optimization.
SILCS Applied to GPCRs
In this GPCR SILCS correctly predicts functional group affinities of a known ligand while offering optimization solutions for this ligand. In addition SILCS has identified novel agonists and a novel allosteric site and allosteric modulators for the beta2-adrenertic receptor.
P38 MAP Kinase FragMaps
FragMaps of P38 MAP Kinase with ligand overlaid on the FragMaps. FragMaps colored by fragment type: green = apolar, red = H-bond acceptor, blue = H-bond donor, orange = negative, and cyan = positive charge. FragMap densities near the bound inhibitor provide options for ligand optimization.
SILCS-SMALL MOLECULE SUITE
The SILCS-SM software suite utilizes the SILCS platform technology to inform and drive small molecule drug design projects at any stage. Our proprietary software has solutions from target validation to lead optimization and more.
SILCS-GUI
The SILCS-GUI provides a point and click approach to protein system preparation and SILCS simulation job submissions for FragMap generation. After the simulations are complete, our FragMaps can be visualized in the SILCS-GUI or your favorite visualization software including Autodock Tools, PyMol, and VMD.
SILCS-MC Capabilities
Utilize the precomputed SILCS FragMaps and the SILCS-GUI to guide your lead compound identification and optimization through rapid ligand docking, pose refinement, and atom-by-atom ligand optimization.
SILCS-Ligand Optimization Video
Discover how the SILCS-GUI can visualize and validate putative binding sites on any region of your target protein and gain insights on draggability and favorable ligand interactions.
Automate your pharmacophore generation to facilitate rapid virtual high throughput screening and ranking of millions of compounds.
SILCS-Ligand Optimization Video
Discover how the SILCS-GUI can visualize and validate putative binding sites on any region of your target protein and gain insights on draggability and favorable ligand interactions.
Automate your pharmacophore generation to facilitate rapid virtual high throughput screening and ranking of millions of compounds.
New point-and-click approach to soluble protein system preparation, iob submission to remote host, job progress tracking, and results visualization.
SILCS: ENHANCED MIXED SOLVENT MD
SILCS: ENHANCED MIXED SOLVENT MD
New point-and-click approach to soluble protein system preparation, iob submission to remote host, job progress tracking, and results visualization.
INSIGHTFUL
SILCS enables discovery of deep binding pockets in proteins, including enzymes and membrane bound proteins such as GPCRs and transporters.
VERSATILE
FragMaps can be used with minimal additional computation to perform Database Screening, Fragment Based Ligand Design & Ligand Optimization.
EASY TO USE
A command-line tool automates setup for transmembrane proteins (GPCRs, transporters and more).
INSIGHTFUL
SILCS enables discovery of deep binding pockets in proteins, including enzymes and membrane bound proteins such as GPCRs and transporters.
VERSATILE
SILCS enables discovery of deep binding pockets in proteins, including enzymes and membrane bound proteins such as GPCRs and transporters.
EASY TO USE
A command-line tool automates setup for transmembrane proteins (GPCRs, transporters and more).
ACCELERATE YOUR RESULTS
WITH SILCSBIO
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