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Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment
October-December 2008 (vol. 5 no. 4)
pp. 525-533
ASCII Text
x 
 
Xueyi Wang, Jack Snoeyink, "Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. 4, pp. 525-533, October-December, 2008.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2008.92,
author = {Xueyi Wang and Jack Snoeyink},
title = {Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {5},
number = {4},
issn = {1545-5963},
year = {2008},
pages = {525-533},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.92},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment
IS - 4
SN - 1545-5963
SP525
EP533
EPD - 525-533
A1 - Xueyi Wang,
A1 - Jack Snoeyink,
PY - 2008
KW - optimization methods
KW - multiple structure alignment
KW - weighted RMSD
KW - structural conserved region
VL - 5
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Xueyi Wang, Northwest Nazarene University, Nampa
Jack Snoeyink, UNC Chapel Hill, Chapel Hill
Pairwise structure alignment commonly uses root mean square deviation (RMSD) to measure the structural similarity, and methods for optimizing RMSD are well established. We extend RMSD to weighted RMSD for multiple structures. By using multiplicative weights, we show that weighted RMSD for all pairs is the same as weighted RMSD to an average of the structures. Thus, using RMSD or weighted RMSD implies that the average is a consensus structure. Although we show that in general, the two tasks of finding the optimal translations and rotations for minimizing weighted RMSD cannot be separated for multiple structures like they can for pairs, an inherent difficulty and a fact ignored by previous work, we develop a near-linear iterative algorithm to converge weighted RMSD to a local minimum. 10,000 experiments of gapped alignment done on each of 23 protein families from HOMSTRAD (where each structure starts with a random translation and rotation) converge rapidly to the same minimum. Finally we propose a heuristic method to iteratively remove the effect of outliers and find well-aligned positions that determine the structural conserved region by modeling B-factors and deviations from the average positions as weights and iteratively assigning higher weights to better aligned atoms.

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Index Terms:
optimization methods, multiple structure alignment, weighted RMSD, structural conserved region
Citation:
Xueyi Wang, Jack Snoeyink, "Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. 4, pp. 525-533, Oct.-Dec. 2008, doi:10.1109/TCBB.2008.92
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