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Bioinformatics Vol. 16 no. 6 2000
Pages 566-567
© 2000 Oxford University Press


Applications Note

DaliLite workbench for protein structure comparison

Liisa Holm 1 and Jong Park 1

1 EMBL-EBI, Cambridge CB10 1SD, UK

Received on November 16, 1999 ; accepted on February 17, 2000

Summary: DaliLite is a program for pairwise structure comparison and for structure database searching. It is a standalone version of the search engine of the popular Dali server. A web interface is provided to view the results, multiple alignments and 3D superimpositions of structures.

Availability: DaliLite has been ported to the Linux and Irix operating systems and can be compiled in many other UNIX operating systems. It is found at http://www.embl-ebi.ac.uk/dali/DaliLite.

Contact: holm{at}embl-ebi.ac.uk


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[Abstract] [Full Text] [PDF]


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