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|Alternative name||Computational Analysis of Novel Drug Opportunities|
|Restrictions to use||None|
|User data submission||Not allowed|
Publications for Computational Analysis of Novel Drug Opportunities
Structure and conformational dynamics of scaffolded DNA origami nanoparticles
[…] f highly structured DNA assemblies programmed using the principle of scaffolded DNA origami remain challenging to predict using these models.As an alternative, here we apply our FE modeling framework CanDo to solve for the ground-state equilibrium structure and mechanical properties of structured DNA nanoparticles. Compared with the aforementioned computational tools, our FE model treats DNA duple […]
Combating Ebola with Repurposed Therapeutics Using the CANDO Platform
[…] (unpublished). This is further supported by our successful initial shotgun multitarget drug repurposing studies that used a different docking with dynamics protocol from what is currently used by the CANDO platform, namely Autodock for docking and NAMD for dynamics simulation [,].The proteomic signature similarity of drugs is then used to rank putative drug candidates for all indications in a shot […]
Lattice free prediction of three dimensional structure of programmed DNA assemblies
[…] ight nucleic acid assemblies in a computationally efficient manner, within the limits imposed by the preceding assumptions.Integration of this procedure into our online structure-prediction framework CanDo will provide a broadly accessible 3D structure-prediction framework that can be refined and extended in the future using high-resolution structural feedback, which can include the detailed explo […]
Data access for the 1,000 Plants (1KP) project
[…] nships at the iPlant site, functional relationships between proteins and their associated metabolites are available from the Computational Biology Group at the University of Washington, developers of CANDO . Sequence similarity-based methods are used to map 1KP proteins to curated repositories of protein-protein interactions (i.e., BioGRID ) and biochemical pathways (i.e., Kyoto Encylopedia of […]
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