Description

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]

Online version (version 1.1, since 20.03.03), currently out of service

Planned to move to bioinformatics.org
simple interface
tutorial for the simple interface
complex interface
paramter files interface

Offline version

Downloads:

• LINUX executables (version 3.4.2 since September 30th 2008)
  • Pentium 4 haystack_pentium4
  • Pentium pro haystack_pentiumpro should run on machine
  • Athlon-XP haystack_athlonxp
  • Intel Xeon Nocona (64 bit) haystack_nocona
• LINUX executables, slightly reduced functionality (no atomtype, importance, orientation, alternative means) but faster
  • Pentium 4 haystack_pentium4_pure
  • Pentium pro haystack_pentiumpro_pure should run on machine
  • Athlon-XP haystack_athlonxp_pure
  • Intel Xeon Nocona (64 bit) haystack_nocona_pure
• Other executables (more machines, other compiler options) can be made upon request!
• Short introduction in Adobe Acrobat format: haystack.pdf or in Postscript: haystack.ps
• Sample parameter files (tar): Params.tar
• Frequently asked questions faq_en, in German: faq_de.