IEEE TRANSACTIONS ON NANOBIOSCIENCE, VOL. X, NO. X, MONTH 2009 1 Towards High-Throughput, Multi-Criteria Protein Structure Comparison Azhar Ali Shah, Gianluigi Folino, and Natalio Krasnogor Manuscript received XXX, 2009; revised XXX, 2009. G. Folino is with the CNR-ICAR, Institute of High Performance Computing and Networking, Italy. E-mail: folino@icar.cnr.it A.A Shah and N. Krasnogor are with the School of Computer Science, University of Nottingham, UK, NG8 1BB. E-mail: {psxaass,Natalio.Krasnogor}@nottingham.ac.uk May 22, 2009 DRAFT