Welcome to SADIC & ProCoCoA
Simple Atom Depth Index Calculator (SADIC) and the Protein Core Composition Analyzer (ProCoCoA) can be run from this server.
If expert settings or processing of large datasets are needed, the resident software implementation of SADIC/ProCoCoa is available for download from our software page
For a given protein structure SADIC calculates depths of each atom as depth index. Atom depth indexes are stored in the B-factor field of modified PDB files. Thus, selected proteins can be analyzed and visualized by using the modified PDB files which can be downloaded from the Results page.
ProCoCoA is a novel algorithm for protein core delineation obtained from atom depth index analysis of residue side chains.
30 September 2013: New visualization for SADIC output, including protein structural layers and overall flexibility prediction.
26 September 2013: Added support for multi-model pdb files (eg NMR bundles).
25 October 2012: SADIC & ProCoCoA server is up and running.
How to cite
Please cite the following references in publications.
Alocci, D., Bernini, A. & Niccolai, N. (2013). Atom depth analysis delineates mechanisms of protein intermolecular interactions. Biochem. Biophys. Res. Commun. 436, 725-729.
Bottini, S., Bernini, A., De Chiara, M, Garlaschelli, D., Spiga, O., Dioguardi, O., Vannuccini, E., Tramontano, A. & and Niccolai, N. (2012). ProCoCoA: a quantitative approach for analyzing protein core composition. Comp. Biol. and Chem. 43, 29-34.
Varrazzo, D., Bernini, A., Spiga, O., Ciutti, A., Chiellini, S., Venditti, V., Bracci, L. & Niccolai, N. (2005). Three-dimensional computation of atom depth in complex molecular structures. Bioinformatics 21, 2856-60.