scholarly journals mTM-align: a server for fast protein structure database search and multiple protein structure alignment

2018 ◽  
Author(s):  
Runze Dong ◽  
Shuo Pan ◽  
Zhenling Peng ◽  
Yang Zhang ◽  
Jianyi Yang
Keyword(s):  
Protein Structure ◽  
Database Search ◽  
Structure Alignment ◽  
Protein Structure Alignment ◽  
Structure Database ◽  
Multiple Protein

ALIGNING MULTIPLE PROTEIN STRUCTURES BY DETERMINISTIC ANNEALING

2005 ◽  
Vol 03 (04) ◽  
pp. 837-860 ◽  
Author(s):  
TIANSHOU ZHOU ◽  
LUONAN CHEN ◽  
YUN TANG ◽  
XIANGSUN ZHANG
Keyword(s):  
Protein Structure ◽  
Structure Prediction ◽  
Protein Structures ◽  
Structure Alignment ◽  
Deterministic Annealing ◽  
Protein Structure Alignment ◽  
Protein Chain ◽  
Fold Family ◽  
Multiple Protein ◽  
Wide Range

Protein structure alignment plays a key role in protein structure prediction and fold family classification. An efficient method for multiple protein structure alignment in a mathematical manner is presented, based on deterministic annealing technique. The alignment problem is mapped onto a nonlinear continuous optimization problem (NCOP) with common consensus chain, matching assignment matrices and atomic coordinates as variables. At each step in the annealing procedure, the NCOP is decomposed into as many subproblems as the number of protein chains, each of which is actually an independent pairwise structure alignment between a protein chain and the consensus chain and hence can be efficiently solved by the parallel computation technique. The proposed method is robust with respect to choice of iteration parameters for a wide range of proteins, and performs well in both multiple and pairwise structure alignment cases, compared with existing alignment methods.

scholarly journals mTM-align: an algorithm for fast and accurate multiple protein structure alignment

2017 ◽  
Vol 34 (10) ◽  
pp. 1719-1725 ◽  
Author(s):  
Runze Dong ◽  
Zhenling Peng ◽  
Yang Zhang ◽  
Jianyi Yang
Keyword(s):  
Protein Structure ◽  
Structure Alignment ◽  
Protein Structure Alignment ◽  
Multiple Protein

scholarly journals mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

2013 ◽  
Vol 32 (4) ◽  
pp. 661-668 ◽  
Author(s):  
Sylvain Léonard ◽  
Agnel Praveen Joseph ◽  
Narayanaswamy Srinivasan ◽  
Jean-Christophe Gelly ◽  
Alexandre G. de Brevern
Keyword(s):  
Protein Structure ◽  
Structure Alignment ◽  
Protein Structure Alignment ◽  
Alignment Method ◽  
Structural Alphabet ◽  
Multiple Protein
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