The computer program NeedleHaystack computes molecular superpositions. A possible large molecule (target=haystack) is scanned for the occurence of a given molecular motif (model=needle) within tolerances. The advance over other methods is that it can handle very large atom sets, e.g. targets of up to 100000 atoms and has not necessarily to include any chemical information and connectivity between atoms: chemical constraints to restrict the solution space are not used to pertain nonobvious superpositions based on geometric fit.
The specialization to the needle-haystack-problem allows a very fast algorithm. Trade-offs between runtime and tolerance levels are possible. The program is fast enough to screen large databases in an acceptable time.
Please cite the following reference when using NeedleHaystack:
Andreas Hoppe and Cornelius Frömmel. NeedleHaystack: A program for the rapid recognition of local structures in large sets of atomic coordinates. J. Appl. Cryst. (2003). 36, 1090-1097. [pdf, ps]
Planned to move to bioinformatics.org
tutorial for the simple interface
paramter files interface
last update: 9th Feb 2009