Welcome to SADIC & ProCoCoA

Simple Atom Depth Index Calculator (SADIC) and the Protein Core Composition Analyzer (ProCoCoA) can be run from this server.
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.

Choose source of structural data:

upload a file in pdb format:

Uploading large PDB files may take minutes, please wait and do not reload page.
Please note that for multi-model PDB's the first model is used.

Choose algorhitm:

SADIC with structural layers

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


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.