BioSolveIT's KNIME components (the entire suite of structure-based design tools) have recently been updated to include our latest addition, SeeSAR, the next-generation structure based drug design tool. With an intuitive user interface, users can quickly and easily load and visualize protein-ligand complexes as well as calculate an estimated binding affinity using our unique, proprietary HYDE scoring technology. Molecules can be edited and rescored on the fly, enabling the user to rapidly explore new ideas. In addition to this, ligand rotatable bonds can be color-coded based on their match to statistical analyses of observed torsion angles, helping the designer to minimize conformational strain.
For more info, google KNIME BioSolveIT (unfortunately giving a URL here catches my message in the spam filters)
As part of this update, a couple more of our tools (Naomi & Coord3D) have had their licence requirement removed, and can now be freely used by all!
Naomi converts molecules between different representations (SDF, Mol2, and SMILES) and can perform substructure-mappings, as well as generation of super-high quality 2D images in different graphic file formats (SVG, PNG) for use in KNIME reports. Naomi can also be registered as molecule renderer within KNIME® - in my opinion the best renderer available!
Coord3D generates high quality 3D coordinates for small molecules based on gold-standard torsion angle data extracted directly from the Cambridge Crystallographic Data Centre's CSD database. Based on smiles, SD or mol2 input, Coord3D will convert and output in 3D in the format of your choice.
The nodes are available via the usual KNIME update mechanism (simply add http://www.biosolveit.de/KNIME/download/biosolveit_knime_nodes to your list of update sites), or via download the entire package from our website
I very much hope that you like our new tools – please feel free to get in touch if you find them useful in your work.
Regards,
Alastair