mTM-align: a server for fast protein structure database search and multiple protein structure alignment
By Runze Dong, Shuo Pan, Zhenling Peng, Yang Zhang, Jianyi Yang. 2018
85 citations recorded by the source corpus.
Abstract With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2–5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.
Subfields: Materials Chemistry, Molecular Biology
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In Materials Chemistry
In Molecular Biology
- Yang Zhang
- Ivan V. Anishchenko
- Zhenling Peng
- David Baker
- Jianyi Yang
- Liisa Holm
- Wenkai Wang
- Zongyang Du
Citations in the corpus
- DALI and the persistence of protein shape (2019, methodology): “27 Figure 2E compares structural alignments by DALI, two other programs 28,29 and a human expert.”
- The trRosetta server for fast and accurate protein structure prediction (2021, methodology): “4e, with estimated TM-score >0.8) does belong to the hotdog fold according to the results by a fast search against the PDB database with the mTM-align server 29 .”