Efficient protein alignment algorithm for protein search

Zaixin Lu, Zhiyu Zhao, Bin Fu

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore protein structure alignment algorithms are very helpful for protein biologists. However, an accurate alignment algorithm itself may be insufficient for effective discovering of structural relationships among tens of thousands of proteins. Due to the exponentially increasing amount of protein structural data, a fast and accurate structure alignment tool is necessary to access protein classification and protein similarity search; however, the complexity of current alignment algorithms are usually too high to make a fully alignment-based classification and search practical.Results: We have developed an efficient protein pairwise alignment algorithm and applied it to our protein search tool, which aligns a query protein structure in the pairwise manner with all protein structures in the Protein Data Bank (PDB) to output similar protein structures. The algorithm can align hundreds of pairs of protein structures in one second. Given a protein structure, the tool efficiently discovers similar structures from tens of thousands of structures stored in the PDB always in 2 minutes in a single machine and 20 seconds in our cluster of 6 machines. The algorithm has been fully implemented and is accessible online at our webserver, which is supported by a cluster of computers.Conclusion: Our algorithm can work out hundreds of pairs of protein alignments in one second. Therefore, it is very suitable for protein search. Our experimental results show that it is more accurate than other well known protein search systems in finding proteins which are structurally similar at SCOP family and superfamily levels, and its speed is also competitive with those systems. In terms of the pairwise alignment performance, it is as good as some well known alignment algorithms.

Original languageEnglish (US)
Article numberS34
JournalBMC Bioinformatics
Volume11
Issue numberSUPPLL.1
DOIs
StatePublished - Jan 18 2010

Fingerprint

Alignment
Proteins
Protein
Protein Structure
Pairwise
Protein Classification
Similarity Search
Web Server
Single Machine
Conformation
Databases
Classify
Query
Necessary
Conformations
Output
Experimental Results

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

Efficient protein alignment algorithm for protein search. / Lu, Zaixin; Zhao, Zhiyu; Fu, Bin.

In: BMC Bioinformatics, Vol. 11, No. SUPPLL.1, S34, 18.01.2010.

Research output: Contribution to journalArticle

Lu, Zaixin ; Zhao, Zhiyu ; Fu, Bin. / Efficient protein alignment algorithm for protein search. In: BMC Bioinformatics. 2010 ; Vol. 11, No. SUPPLL.1.
@article{83de4d4f62fc4ee8bbafcb18b87b0f68,
title = "Efficient protein alignment algorithm for protein search",
abstract = "Background: Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore protein structure alignment algorithms are very helpful for protein biologists. However, an accurate alignment algorithm itself may be insufficient for effective discovering of structural relationships among tens of thousands of proteins. Due to the exponentially increasing amount of protein structural data, a fast and accurate structure alignment tool is necessary to access protein classification and protein similarity search; however, the complexity of current alignment algorithms are usually too high to make a fully alignment-based classification and search practical.Results: We have developed an efficient protein pairwise alignment algorithm and applied it to our protein search tool, which aligns a query protein structure in the pairwise manner with all protein structures in the Protein Data Bank (PDB) to output similar protein structures. The algorithm can align hundreds of pairs of protein structures in one second. Given a protein structure, the tool efficiently discovers similar structures from tens of thousands of structures stored in the PDB always in 2 minutes in a single machine and 20 seconds in our cluster of 6 machines. The algorithm has been fully implemented and is accessible online at our webserver, which is supported by a cluster of computers.Conclusion: Our algorithm can work out hundreds of pairs of protein alignments in one second. Therefore, it is very suitable for protein search. Our experimental results show that it is more accurate than other well known protein search systems in finding proteins which are structurally similar at SCOP family and superfamily levels, and its speed is also competitive with those systems. In terms of the pairwise alignment performance, it is as good as some well known alignment algorithms.",
author = "Zaixin Lu and Zhiyu Zhao and Bin Fu",
year = "2010",
month = "1",
day = "18",
doi = "10.1186/1471-2105-11-S1-S34",
language = "English (US)",
volume = "11",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",
number = "SUPPLL.1",

}

TY - JOUR

T1 - Efficient protein alignment algorithm for protein search

AU - Lu, Zaixin

AU - Zhao, Zhiyu

AU - Fu, Bin

PY - 2010/1/18

Y1 - 2010/1/18

N2 - Background: Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore protein structure alignment algorithms are very helpful for protein biologists. However, an accurate alignment algorithm itself may be insufficient for effective discovering of structural relationships among tens of thousands of proteins. Due to the exponentially increasing amount of protein structural data, a fast and accurate structure alignment tool is necessary to access protein classification and protein similarity search; however, the complexity of current alignment algorithms are usually too high to make a fully alignment-based classification and search practical.Results: We have developed an efficient protein pairwise alignment algorithm and applied it to our protein search tool, which aligns a query protein structure in the pairwise manner with all protein structures in the Protein Data Bank (PDB) to output similar protein structures. The algorithm can align hundreds of pairs of protein structures in one second. Given a protein structure, the tool efficiently discovers similar structures from tens of thousands of structures stored in the PDB always in 2 minutes in a single machine and 20 seconds in our cluster of 6 machines. The algorithm has been fully implemented and is accessible online at our webserver, which is supported by a cluster of computers.Conclusion: Our algorithm can work out hundreds of pairs of protein alignments in one second. Therefore, it is very suitable for protein search. Our experimental results show that it is more accurate than other well known protein search systems in finding proteins which are structurally similar at SCOP family and superfamily levels, and its speed is also competitive with those systems. In terms of the pairwise alignment performance, it is as good as some well known alignment algorithms.

AB - Background: Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore protein structure alignment algorithms are very helpful for protein biologists. However, an accurate alignment algorithm itself may be insufficient for effective discovering of structural relationships among tens of thousands of proteins. Due to the exponentially increasing amount of protein structural data, a fast and accurate structure alignment tool is necessary to access protein classification and protein similarity search; however, the complexity of current alignment algorithms are usually too high to make a fully alignment-based classification and search practical.Results: We have developed an efficient protein pairwise alignment algorithm and applied it to our protein search tool, which aligns a query protein structure in the pairwise manner with all protein structures in the Protein Data Bank (PDB) to output similar protein structures. The algorithm can align hundreds of pairs of protein structures in one second. Given a protein structure, the tool efficiently discovers similar structures from tens of thousands of structures stored in the PDB always in 2 minutes in a single machine and 20 seconds in our cluster of 6 machines. The algorithm has been fully implemented and is accessible online at our webserver, which is supported by a cluster of computers.Conclusion: Our algorithm can work out hundreds of pairs of protein alignments in one second. Therefore, it is very suitable for protein search. Our experimental results show that it is more accurate than other well known protein search systems in finding proteins which are structurally similar at SCOP family and superfamily levels, and its speed is also competitive with those systems. In terms of the pairwise alignment performance, it is as good as some well known alignment algorithms.

UR - http://www.scopus.com/inward/record.url?scp=76549117710&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=76549117710&partnerID=8YFLogxK

U2 - 10.1186/1471-2105-11-S1-S34

DO - 10.1186/1471-2105-11-S1-S34

M3 - Article

C2 - 20122207

AN - SCOPUS:76549117710

VL - 11

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

IS - SUPPLL.1

M1 - S34

ER -