scholarly journals Dali server: conservation mapping in 3D

2010 ◽  
Vol 38 (suppl_2) ◽  
pp. W545-W549 ◽  
Author(s):  
Liisa Holm ◽  
P�ivi Rosenstr�m
Keyword(s):  
Dali Server

scholarly journals Dali server update

2016 ◽  
Vol 44 (W1) ◽  
pp. W351-W355 ◽  
Author(s):  
Liisa Holm ◽  
Laura M. Laakso
Keyword(s):  
Dali Server

scholarly journals Comparison of proteins based on segments structural similarity.

2004 ◽  
Vol 51 (1) ◽  
pp. 161-172 ◽  
Author(s):  
Dariusz Plewczynski ◽  
Jakub Pas ◽  
Marcin Von Grotthuss ◽  
Leszek Rychlewski
Keyword(s):  
Structure Prediction ◽  
Structural Alignment ◽  
Structural Similarity ◽  
Data Bank ◽  
Simple Method ◽  
Accurate Comparison ◽  
Scop Classification ◽  
Prediction Evaluation ◽  
Dali Server ◽  
Speed And Accuracy

We present here a simple method for fast and accurate comparison of proteins using their structures. The algorithm is based on structural alignment of segments of Calpha chains (with size of 99 or 199 residues). The method is optimized in terms of speed and accuracy. We test it on 97 representative proteins with the similarity measure based on the SCOP classification. We compare our algorithm with the LGscore2 automatic method. Our method has the same accuracy as the LGscore2 algorithm with much faster processing of the whole test set, which is promising. A second test is done using the ToolShop structure prediction evaluation program and shows that our tool is on average slightly less sensitive than the DALI server. Both algorithms give a similar number of correct models, however, the final alignment quality is better in the case of DALI. Our method was implemented under the name 3D-Hit as a web server at http://3dhit.bioinfo.pl/ free for academic use, with a weekly updated database containing a set of 5000 structures from the Protein Data Bank with non-homologous sequences.

Sign in / Sign up

Export Citation Format

Share Document