SilcsBio - Version SILCS - Site-Identification Software
Site-Identification by Ligand Competitive Saturation (SILCS) generates 3-D maps (FragMaps) of interaction patterns for chemical functional groups with your target molecule.
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INNOVATIVE LIGAND DESIGN & OPTIMIZATION WITH SILCS
Site-Identification by Ligand Competitive Saturation (SILCS) generates 3-D maps (FragMaps) of interaction patterns for chemical functional groups vvith your target molecule.
SILCS reveals intricacies of dynamics and provides tools to optimize ligand scaffolds using qualitative and quantitative binding pockets insights allowing more rapid and effective drug design.
SILCS: ENHANCED MIXED SOLVENT MD
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.
LET FRAGMAPS GUIDE YOUR LEAD DISCOVERY
Conveniently explore FragMaps in our user interface or in your favorite molecular visualization software, including Autodock Tools, Pymol MOE, and VMD.
Visualize favorable interactions with the target macromolecule.
Gain insights to design better ligands with optimally placed functional groups.
FragMap of p38 MAP kinase-ligand complex colored by fragment type: green = apolar, red = H-bond acceptor, blue = H-bond donor & cyan = positive charge. FragMap densities near the bound inhibitor provide options of ligand optimization.
USER INTERFACE
New point-and-click approach to soluble protein system is preparation, job submission to remote host and progress tracking, and results visualization.
INSIGHTFUL
SILCS enables discovery of deep binding pockets in proteins & enzymes including membrane bound proteins.
In this GPCR SILCS correctly predicts functional group affinities of a known ligand while simultaneously offering optimization solutions for this ligand. This approach has identified novel agonists of the β2-Adrenergic Receptor.
VERSATILE
SILCS enables discovery of deep binding pockets in proteins & enzymes including membrane bound proteins.
EASY TO USE
A command-line tool automates setup for transmembrane proteins (GPCRs and more).
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