EDIAscorer
Overview
The electron density score for individual atoms (EDIA) quantifies the electron density fit of each atom in a crystallographically resolved structure. Multiple EDIA values can be combined using the power mean to compute the EDIAm, i.e., the electron density score for a group of several atoms. It enables users to score a set of atoms, such as a ligand, a residue, or an active site.
Method
The EDIA value is the weighted mean over all relevant grid points in the sphere of interest around the atom. The radius of the sphere of interest is two times the resolution-dependent electron density sphere radius. EDIA values above 0.8 mark well-supported atoms. EDIA values below 0.8 mark atoms that users should visually inspect in more detail as they are inconsistent with the electron density.
The EDIAm describes the density fit of residues such as protein residues or ligands. Due to the power mean, an EDIAm below 0.8 has at least one atom with an EDIA below 0.3 or three atoms with EDIA values below 0.4. Substructures with an EDIAm below 0.8 should be visually inspected. Depending on the use case, higher or lower EDIAm values might be tolerable.
Software Availability
We are offering EDIAscorer as part of our ProteinsPlus web service. There, users can analyze all PDB structures with electron density deposited in the PDB. Please visit https://proteins.plus, upload your protein, and choose EDIAscorer.
The command-line tool EDIAscorer is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download EDIAscorer, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run EDIAscorer. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.
References
Meyder, A.; Nittinger, E.; Lange, G.; Klein, R.; Rarey, M. Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. J Chem Inf Model 2017, 57 (10), 2437-2447. DOI: https://doi.org/10.1021/acs.jcim.7b00391
Nittinger, E.; Schneider, N.; Lange, G.; Rarey, M. Evidence of water molecules--a statistical evaluation of water molecules based on electron density. J Chem Inf Model 2015, 55 (4), 771-783. DOI: https://doi.org/10.1021/ci500662d