Improve version of TOP

Guoguang LU guoguang at ALFA.MBB.KI.SE
Wed Feb 4 15:39:27 EST 1998


	Improve version of the TOP software package for automatic comparison
			of 3-d protein structures

The TOP program for automatic comparisons of protein structures has been 
recently improved. The new version for unix computers can be obtained via FTP. 
The new version of Web server has been also installed. Please see 
http://gamma.mbb.ki.se/~guoguang/webtop/wwwtop.html

The most significant improvement is in seraching similar structures in database.
The users of old version complained that the program output too much 
infomration (noise) which is diffult to get the point. The new version
gives parameters of "Structure Diveristy" and "Topological Diversity"
which rank the similarity between homologous structures. It is much
easier for users to find the their most similar structures in the
search and igore the noise.

The new version is able to find sequence permutations in the comparisons
This will help to find homologous structures which is missed the other 
software with similar functions. 

Some part of the document mightbe quite confusing. I need feed back from 
users to fix it. It is also very welcome to complain about any problem of 
Web server and the unix verison. 

Guoguang

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Guoguang Lu, PhD, Research Scientist
Division of Molecular Structural Biology	
Department of Medical Biochemistry and Biophysics 
Doktorsringen 9A1
Karolinska Institute
17177 Stockholm
Sweden
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Phone: (int+46)-8-728 7651(o)   Email:    guoguang at alfa.mbb.ki.se
Fax:   (int+46)-8-327626   Homepage: http://gamma.mbb.ki.se/~guoguang
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