This is a sequence of matching pairs of SSEs, one for each SSE in the pattern, where first member is an SSE from the diagram and the second is an SSE from the pattern. We can describe the result of matching by the the correspondence and also a list of the total number of inserts between adjacent members of the SSE sequence in the diagram. A pattern may match a diagram in none or more ways and may match none or more diagrams in a given database of diagrams. The TOPS query system is accessed over the Web using an HTML form, and there is on-line help. Users can select several output parameters, the order in which they are output for each successful match, and whether to sort on these.
Output is incremental unless sorting is selected.
Output parameters include domain name , CATH-number , matching node numbers , and sum of inserts between the nodes. Alternatively, users can construct their own query patterns based on the sequence of SSEs and associated inserts and the associated sets of H-bonds and chiralities. Acknowledgements We are grateful to Dr. T. P. Flores for giving us the source code for TOPS and allowing us to modify it without restriction. We are also grateful to Dr. C. A. Orengo for providing us with the domain boundary file associated with the CATH 3 protein structural domain classification. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B.,Meyer Jr., E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol.