Multiple pairwise surface comparison. MolLoc also allows multiple pairwise surface comparison of one query struc- ture with up to 20 other structures. Here, the email address is mandatory. For the query structure, the user can still specify a PDB ID or upload a structure. The preprocessing phase (chain selection and atoms selection) works like in the pairwise case. The list of other structures must belong to the PDB, and the user can specify the chain(s) using the syntax pdb_id,chain(s) (e.g. 1atp, EI). For these other structures, MolLoc automatically selects all of their binding sites for comparison with the query structure. Processing method The web server is built upon a method for the discovery of similar regions on two molecular surfaces based on a spin- image representation of the surfaces (17). Given two struc- tures, the only geometry method: (1) builds their Connolly’s molecular surfaces (18); (2) builds the spin-image representations of Connolly’s points (19); (3) compares the spin images of the atoms of the two surfaces, and puts them in correspondence if their correlation is high (>0.5); (4) ﬁnds sets of geometrically consistent correspondences using a greedy procedure; (5) the largest set of correspondences represents the best solution; (6) the obtained point correspondences are given as input to the Horn method (20) that produces the best rototranslation that superimposes the two regions. The geometry + atomtype method takes as input the superimposition obtained with the only geometry method, and checks for atoms of the ﬁrst structure that are closer than 2.5 A˚ to at least one atom with the same atomtype (16) belonging to the second structure. The atomtypes are deﬁned for protein atoms only, and corre- spond to the following properties: hydrogen-bond donor (DON), hydrogen-bond acceptor (ACC), mixed donor/ acceptor (DAC), hydrophobic aliphatic (ALI) and aro- matic contacts (PI). Then, the method keeps all the pairs of atoms that are unambiguous, where a pair (Ai, Bj) of atoms Ai in the ﬁrst structure and Bj in the second struc- ture is unambiguous if Bj is the only atom that is closer than 2.5 A˚ to Ai, and vice versa. These n pairs are given in input to the Horn’s method, that produces a second roto- translation. Again, the method checks for unambiguous atom pairs. If the number m of the new set of pairs is such that m > n, then the procedure iterates (for a maximum of 10 steps), else it stops. The cavity detection procedure is a novel method that allows the fast determination of cavities with adjustable depth. The method consists of the following steps: (1) for each atom i belonging to the surface, count the number of atom centers NC(i) that lie within a radius R from the center of i; Nucleic Acids Research, 2009, Vol. 37, Web Server issue W567 Figure 3. (a) Cavities of cystic ﬁbrosis transmembrane conductance regulator with R = 12; (b) cavity of the human chaperon hsp90 with R = 20. (2) the cavity atoms are deﬁned as those atoms i s.t. NC(i) m(NC) + s(NC), where m(NC) is the mean, s(NC) is the standard deviation and = 0.5. The cavity size and topology depends on the value of radius R (Figure 3). In MolLoc, the choices are R = 4, 8, 12, 20, where R = 4 is for shallow cavities and R = 20 is for very deep cavities. Output of the web server The top of the results page presents the statistics of the experiment: number of selected input atoms in each struc- ture, ratio of corresponding surface area to the selected input surface area in each structure, number of corre- sponding atoms with the same atomtype between the two structures, together with their RMSD. Furthermore, the page allows the download of the ﬁrst PDB ﬁle by clicking on its protein name at the top of the right-hand column, the second PDB ﬁle rototranslated after the superimposition by clicking on its protein name in the right-hand column, the matrix of rototranslation in