PMID- 16078364
OWN - NLM
STAT- MEDLINE
DCOM- 20051129
LR  - 20191210
IS  - 0219-7200 (Print)
IS  - 0219-7200 (Linking)
VI  - 3
IP  - 4
DP  - 2005 Aug
TI  - Aligning multiple protein structures by deterministic annealing.
PG  - 837-60
AB  - 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 sub-problems 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.
FAU - Zhou, Tianshou
AU  - Zhou T
AD  - School of Mathematics and Computational Sciences, Zhongshan University, Guangzhou 
      510275, China. mcszhtsh@zsu.edu.cn
FAU - Chen, Luonan
AU  - Chen L
FAU - Tang, Yun
AU  - Tang Y
FAU - Zhang, Xiangsun
AU  - Zhang X
LA  - eng
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - Singapore
TA  - J Bioinform Comput Biol
JT  - Journal of bioinformatics and computational biology
JID - 101187344
RN  - 0 (Proteins)
SB  - IM
MH  - *Algorithms
MH  - Amino Acid Sequence
MH  - Computer Simulation
MH  - *Models, Molecular
MH  - Molecular Sequence Data
MH  - Numerical Analysis, Computer-Assisted
MH  - Proteins/*analysis/*chemistry
MH  - Sequence Alignment/*methods
MH  - Sequence Analysis, Protein/*methods
EDAT- 2005/08/04 09:00
MHDA- 2005/12/13 09:00
CRDT- 2005/08/04 09:00
PHST- 2004/07/12 00:00 [received]
PHST- 2004/12/30 00:00 [accepted]
PHST- 2005/08/04 09:00 [pubmed]
PHST- 2005/12/13 09:00 [medline]
PHST- 2005/08/04 09:00 [entrez]
AID - S0219720005001351 [pii]
AID - 10.1142/s0219720005001351 [doi]
PST - ppublish
SO  - J Bioinform Comput Biol. 2005 Aug;3(4):837-60. doi: 10.1142/s0219720005001351.