This program implements the multiple target similarity algorithms of Willett et al against a Daylight merlin pool.
The program operates in two major modes.
For each target, the pool is sorted by similarity and the user-defined number of neighbours retained.
These lists are fused by sorting them on either best rank or best similarity value against any target. Fusing in this way ensures that the original targets are retained in the final hit list.
Optional outputs are
Key literature references:
Whittle, M., Gillet, V.J., Willett, P., Alex, A. & Losel, J. "Enhancing
the effectiveness of virtual screening by fusing nearest-neighbour lists:
a comparison of similarity coefficients" Journal of Chemical
Information and Computer Sciences 2004 44,1840-1848
Hert, J., Willett, P., Wilton, D.J., Acklin, P., Azzaoui, K., Jacoby, E. & Schuffenhauer, A. "Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures" Journal of Chemical Information and Computer Sciences 2004 44, 1177-1185
Hert, J., Willett, P., Wilton, D.J., Acklin, P., Azzaoui, K., Jacoby, E. & Schuffenhauer, A. "Topological descriptors for similarity-based virtual screening using multiple bioactive reference structures" Organic and Biomolecular Chemistry 2004 2(22), 3256-3266
Program multimer. Calling syntax: $ multimer [options] databasename Options:- -t <n> the number of targets.(10) -f <n> the maximum size of the final hitlist.(125) -n <n> the number of neighbours to consider for each target.(50) Defaults are in parentheses -turbo creates the target list by similarity to a single input SMILES Default is FALSE -ranks create the output based on rank rather than value (default) -tdt creates output as a file of SMILES in tdt format which will read directly into xvmerlin -smiles prints the space delimited SMILES followed by the best similarity value or rank Default is a tab delimited table:- Compound_ID Best_rank Best_similarity Sum_of_ranks Count_of_ranks SMILES -dos produces output with cr/lf at the end of each data line to facilitate transfer to a Windows statistics package Default is FALSE i.e. unix output This program reads SMILES on stdin and returns the user requested output on stdout. Database specification format is: database%basepw@host:service:user%user-hostpw The database name must be specified (other fields are optional).