Published online 22 April 2005
Article |
TM-align: a protein structure alignment algorithm based on the TM-score
Center of Excellence in Bioinformatics, University at Buffalo 901 Washington Street, Buffalo, NY 14203, USA
*To whom correspondence should be addressed. Tel: +1 716 849 6712; Fax: +1 716 849 6747; Email: skolnick{at}buffalo.edu
Received March 5, 2005. Revised April 1, 2005. Accepted April 1, 2005.
We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is 
4 times faster than CE and 20 times faster than DALI and SAL. On average, the resulting structure alignments have higher accuracy and coverage than those provided by these most often-used methods. TM-align is applied to an all-against-all structure comparison of 10 515 representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff <95%: 1996 distinct folds are found when a TM-score threshold of 0.5 is used. We also use TM-align to match the models predicted by TASSER for solved non-homologous proteins in PDB. For both folded and misfolded models, TM-align can almost always find close structural analogs, with an average root mean square deviation, RMSD, of 3 Å and 87% alignment coverage. Nevertheless, there exists a significant correlation between the correctness of the predicted structure and the structural similarity of the model to the other proteins in the PDB. This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at http://bioinformatics.buffalo.edu/TM-align.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Pei, B.-H. Kim, and N. V. Grishin PROMALS3D: a tool for multiple protein sequence and structure alignments Nucleic Acids Res., April 1, 2008; 36(7): 2295 - 2300. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Chen and J. Skolnick M-TASSER: An Algorithm for Protein Quaternary Structure Prediction Biophys. J., February 1, 2008; 94(3): 918 - 928. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Cheng, B.-H. Kim, and N. V. Grishin MALISAM: a database of structurally analogous motifs in proteins Nucleic Acids Res., January 11, 2008; 36(suppl_1): D211 - D217. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Brylinski and J. Skolnick A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation PNAS, January 8, 2008; 105(1): 129 - 134. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. S. Domingues, J. Rahnenfuhrer, and T. Lengauer Conformational analysis of alternative protein structures Bioinformatics, December 1, 2007; 23(23): 3131 - 3138. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Meyerguz, J. Kleinberg, and R. Elber From the Cover: The network of sequence flow between protein structures PNAS, July 10, 2007; 104(28): 11627 - 11632. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. B. Pandit, Y. Zhang, and J. Skolnick TASSER-Lite: An Automated Tool for Protein Comparative Modeling Biophys. J., December 1, 2006; 91(11): 4180 - 4190. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Maupetit, R. Gautier, and P. Tuffery SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W147 - W151. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhang, I. A. Hubner, A. K. Arakaki, E. Shakhnovich, and J. Skolnick On the origin and highly likely completeness of single-domain protein structures PNAS, February 21, 2006; 103(8): 2605 - 2610. [Abstract] [Full Text] [PDF]
|
|