Buy article online - an online subscription or single-article purchase is required to access this article.
Download citation
Download citation
link to html
A program that computes molecular superpositions is presented. A possible large molecule (target = haystack) is scanned for the occurrence 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 does not necessarily require any chemical information and connectivity between atoms: chemical constraints to restrict the solution space are not used to relate non-obvious superpositions based on a geometric fit. The specialization to a needle-in-a-haystack problem allows a very fast algorithm. Trade-offs between run time and tolerance levels are possible. The program is fast enough to screen large databases in an acceptable time. An executable for Linux on Pentium-compatible machines is available free of charge at http://www.charite.de/bioinf/haystack . It is a command-line executable well suited for scripts and distributed computing. A Web interface for immediate testing is also available at this address.

Subscribe to Journal of Applied Crystallography

The full text of this article is available to subscribers to the journal.

If you have already registered and are using a computer listed in your registration details, please email support@iucr.org for assistance.

Buy online

You may purchase this article in PDF and/or HTML formats. For purchasers in the European Community who do not have a VAT number, VAT will be added at the local rate. Payments to the IUCr are handled by WorldPay, who will accept payment by credit card in several currencies. To purchase the article, please complete the form below (fields marked * are required), and then click on `Continue'.
E-mail address* 
Repeat e-mail address* 
(for error checking) 

Format*   PDF (US $40)
   HTML (US $40)
   PDF+HTML (US $50)
In order for VAT to be shown for your country javascript needs to be enabled.

VAT number 
(non-UK EC countries only) 
Country* 
 

Terms and conditions of use
Contact us

Follow J. Appl. Cryst.
Sign up for e-alerts
Follow J. Appl. Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds