What is NCIweb?
NCIweb is a web implementation of the popular
NCIplot code. At the moment,
NCIweb works with promolecular densities. It provides a representation of the non-covalent interactions of a system based on the reduced density gradient of the electron density. More information on the
NCIplot code and the theoretical background of the method can be found
here.
What do I need to use NCIweb?
To use
NCIweb you simply need a PDB or XYZ structure to upload, on which the analysis will be performed. You can also fetch a PDB file directly with its PDB ID. Only single structure PDBs are accepted (not NMR ensembles). If everything works fine, you will receive an email with a link to
NCIwebResults web site. You will find an interface to visualize your results as well as the possibility to download all the result files including a simple
VMD script for visualization. Three operation modes are available:
- Running in Intramolecular mode will study all non-covalent interactions in the system.
- Running in Intermolecular mode will require manual definition of two fragments, and will only study interactions between them.
- Running in Ligand mode will require manual definition of a ligand and a receptor, and will only study interactions between the ligand and the receptor in the proximity.
For PDB files only, additional options are available:
- The clean structure checkbox will selectively remove non-protein fragments from the structure, enabling more processing options.
- The protonate protein checkbox will add hydrogens to the protein using OpenBabel.
- The protonate ligands checkbox will add hydrogens to the ligands using OpenBabel. This may fail for some molecules.
- The preselected ligands checkbox will assume that the ligands to be preserved have been signaled with residue id's LIG1, LIG2 etc. in the input PDB file. This will skip visual selection of ligands.
With our preprocessing pipeline, a PDB structure from a data bank may be directly analyzed. Nevertheless, we recommend manual and careful preparation and protonation whenever possible.
* Only available if data is updated in PDB format.
