SPACE description

This server includes tools for predicting and analyzing structures of biomolecules and their complexes. Our approach is based on surface complementarity (shape and chemical compatibility) of interacting surfaces. Major body of the suggested tools consists of the set of servers and programs:

1. Servers provide: analysis of ligand-protein contacts and contacts of structural units (LPC/CSU); structural analysis of point mutations (MutaProt); side chain modeling (SCCOMP); building the crystal environment of a given PDB file and analysis of crystal contacts (CryCo); contact map analysis (CMA); and predicting transition metal-binding sites using protein structure (CHED) or sequence data (SeqCHED).

2. Programs include: molecular docking (LIGIN); ligand-protein contact analysis (LPC); Analysis of contact of structural units in biomolacules (CSU); side chain modeling (SCCOMP). Output of LPC and CSU is in the simple text format and permits further using it as an input for different programs in order to answer questions interesting to the user.

Reference: Sobolev V., Eyal E., Gerzon S., Potapov V., Babor M., Prilusky J., Edelman M. (2005) SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucl. Acids Res., 33, W39-W43.