W570 Nucleic Acids Research, 2009, Vol. 37, Web Server issue The surface determination routine scales linearly with the number of atoms, ranging from a few seconds for ordinary structures (e.g. 1atp, chain E) to minutes for huge macromolecular complexes (e.g. 1aei, all chains). Therefore, each time the user provides one or more new chains from the PDB, their surface representations are saved into an internal database, to avoid rebuilding when the same chains are invoked again. The surface comparison routine is the most time- consuming module on the web server. Its time complexity is O(n m), where n,m are the number of atoms selected in the ﬁrst and the second structure. The execution time ranges from a few seconds for comparison of medium- sized binding sites (e.g. the binding site of ATP in 1atp,E with the binding site of ATP in 1csn,A) to minutes for comparison of extended areas (e.g. residues 15–350 of 1atp,E with residues 6–298 of 1csn,A). CONCLUSION We have presented MolLoc, a new server for the structural comparison of molecular surfaces. The server allows com- parison of binding sites, cavities and any arbitrary residue selection. The adopted approach is both local and surface- oriented, and therefore it can be particularly useful when testing if molecules with diﬀerent sequences and folds share any local surface similarity. FUNDING Funding for open access charge: Progetto di Ateneo, Universita’ degli Studi di Padova, and Progetto CARIPARO, Padova. Conﬂict of interest statement. None declared. REFERENCES 1. Orengo,C.A. and Taylor,W.R. (1996) SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol., 266, 617–635. 2. Gerstein,M. and Levitt,M. (1998) Comprehensive assessment of automatic structural alignment against a manual standard, the scop classiﬁcation of proteins. Protein Sci., 7, 445–456. 3. Holm,L. and Sander,C. (1995) Dali: a network tool for protein structure comparison. 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