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 <[email protected]> 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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
