W566 Nucleic Acids Research, 2009, Vol. 37, Web Server issue Figure 1. Home page of MolLoc. The user can run a pairwise surface comparison between two structures, or a multiple pairwise surface comparison between a query structure and a list of structures from the PDB. In the latter case, the email address is mandatory. Figure 2. Atoms selection. The user has to provide a nonempty selection of atoms for each structure. Pairwise surface comparison. In the pairwise surface com- parison, MolLoc takes in input the coordinate ﬁles of two molecules in PDB format (14). The user can either insert the pdb-ids of structures that belong to the PDB or upload his/her own structures. Optionally, the user can write his/ her email address, to receive a link to the results at the end of the computation. Next, the user speciﬁes one or more chains from each structure. The third step is the selection of the regions to compare (Figure 2). For each structure, the user can select one or more binding sites, cavities or any set of residues. A ligand is an HETATM residue diﬀerent than HOH in the pdb ﬁle, and the binding site for a ligand L in a structure S is deﬁned as the subset of atoms of S that are closer than 6 A˚ to at least one atom of L. The cavities are generated with dif- ferent depths, ranging from shallow cavities to very deep cavities. Each structure is associated to a Jmol visualiza- tion (15), thus enabling the user to visualize the selected regions. Finally, the user can choose the comparison method. The method called only geometry does not make use of any physicochemical property, while the method called geometry + atomtype starts from the roto- translation obtained with the purely geometrical method and iteratively reﬁnes it by matching pairs of atoms with the same atomtype, as speciﬁed in (16). The atomtypes are deﬁned only for protein atoms, and therefore the second method is speciﬁc for the comparison of two proteins.