Multiple Alignment of Structures Using Center Of ProTeins

@inproceedings{Roy2015MultipleAO,
  title={Multiple Alignment of Structures Using Center Of ProTeins},
  author={Kaushik Roy and Satish Panigrahi and Asish Mukhopadhyay},
  booktitle={ISBRA},
  year={2015}
}
In this paper we report on an algorithm for aligning multiple protein structures. The algorithm has been tested on a variety of inputs and it performs well in comparison to well-known algorithms for this problem. 
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References

SHOWING 1-10 OF 79 REFERENCES
Multiple Alignment of Protein Structures in Three Dimensions
TLDR
The paper describes the algorithm of multiple alignment of protein structures in 3D used in the EBI-MSD web service SSM (Secondary Structure Matching) located at URL given in the title, based on an efficient SSM algorithm for pairwise structure alignment.
The Shape and Structure of Proteins
TLDR
This image shows the overall organization of the polypeptide chain and Ribbon is an easy way to visualize secondary structures, such as a helices and b sheets.
Multiple Alignment of protein structures and sequences for VMD
Multiple Alignment is a new interface for performing and analyzing multiple protein structure alignments. It enables viewing levels of sequence and structure similarity on the aligned structures and
An Eigendecomposition Method for Protein Structure Alignment
TLDR
This paper model a protein as a polygonal chain of α carbon residues in three dimension and investigates the application of an eigendecomposition method due to Umeyama to the protein structure alignment problem, which allows to reduce the structural alignment problem to an approximate weighted graph matching problem.
Recent progress in multiple sequence alignment: a survey.
TLDR
In this review, existing techniques are described and the potential strengths and weaknesses of the most widely used multiple alignment packages are exposed.
Amino acid substitution matrices from protein blocks.
  • S. HenikoffJ. Henikoff
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1992
TLDR
This work has derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins, leading to marked improvements in alignments and in searches using queries from each of the groups.
Algorithmic aspects of protein structure similarity
TLDR
These are the first approximation algorithms with guaranteed error bounds, and NP-completeness results in the literature in the area of protein structure alignment/fold recognition for measures of structure similarity of practical interest.
MultiProt - A Multiple Protein Structural Alignment Algorithm
TLDR
A fully automated highly efficient technique which detects the multiple structural alignments of protein structures and presents new multiple structural alignment results of protein families from the All beta proteins class in the SCOP classification.
mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet
TLDR
A new web server is proposed called multiple Protein Block Alignment (mulPBA), which implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles, enabling the use of powerful sequence alignment methods for primary structure comparison.
Multiple structure alignment and consensus identification for proteins
TLDR
A comparison with other coordinate-based alignment algorithms shows that the proposed algorithm is competitive in terms of speed and the sizes of the conserved regions discovered in an extensive benchmark dataset derived from the HOMSTRAD and SABmark databases.
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