[med-svn] r5870 - trunk/packages/tm-align/trunk/debian

[Andreas Tille]

Author: tille
Date: 2011-02-03 12:52:39 +0000 (Thu, 03 Feb 2011)
New Revision: 5870

Added:
   trunk/packages/tm-align/trunk/debian/README.Debian
   trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml
Log:
Added some docs to TM-align


Added: trunk/packages/tm-align/trunk/debian/README.Debian
===================================================================
--- trunk/packages/tm-align/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/tm-align/trunk/debian/README.Debian	2011-02-03 12:52:39 UTC (rev 5870)
@@ -0,0 +1,38 @@
+README.Debian for TMalign and TMScore
+-------------------------------------
+
+The homepage of TM-align (http://zhanglab.ccmb.med.umich.edu/TM-align/) says:
+
+	TM-align is a computer algorithm for protein structure alignment using
+	dynamic programming and TM-score rotation matrix. An optimal alignment
+	between two proteins, as well as the TM-score, will be reported for each
+	comparison. The value of TM-score lies in (0,1]. In general, a
+	comparison of TM-score < 0.2 indicates that there is no similarity
+	between two structures; a TM-score > 0.5 means the structures share the
+	same fold. 
+
+The homepage of TM-score (http://zhanglab.ccmb.med.umich.edu/TM-score/) says:
+
+	TM-score is an algorithm to calculate the similarity of topologies of
+	two protein structures. It can be exploited to quantitatively access the
+	quality of protein structure predictions relative to native. Because
+	TM-score weights the close matches stronger than the distant matches,
+	TM-score is more sensitive than root-mean-square deviation (RMSD) (An
+	illustative example can be found from here). A single score between
+	(0,1] is assigned to each comparison. Based on statistics, if a
+	template/model has a TM-score around or below 0.17, it means the
+	prediction is nothing more than a random selection from PDB library.
+
+The difference between both programs is explained as follows:
+
+	What is the difference between TM-score and TM-align? The TM-score
+	program is to compare two models based on their given and known residue
+	equivalency. It is usually NOT applied to compare two proteins of
+	different sequences. The TM-align is a structural alignment program for
+	comparing two proteins whose sequences can be different. The TM-align
+	will first find the best equivalent residues of two proteins based on
+	the structure similarity and then output a TM-score. The TM-score values
+	in both programs have the same definition.
+
+ -- Andreas Tille <tille at debian.org>  Sun, 30 Jan 2011 22:49:21 +0100
+

Added: trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml	2011-02-03 12:52:39 UTC (rev 5870)
@@ -0,0 +1,15 @@
+Contact: Yang Zhang <zhng at umich.edu>
+DOI: 10.1093/nar/gki524
+Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/
+PMID: 15849316
+Name: TM-align & TM-score
+Reference:
+ AUTHOR: Y. Zhang, J. Skolnick
+ TITILE: TM-align: A protein structure alignment algorithm based on TM-score
+ JOURNAL: Nucleic Acids Research
+ YEAR: 2005
+ PAGES: 2302-2309
+ VOLUME: 33
+ NUMBER: 7
+ URL: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf
+ ISSN: 1362-4962