\textit{Pin-Align}: a new dynamic programming approach to align protein-protein interaction networks

DOI10.1155/2014/393908MaRDI QIDQ2330152zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Farid Amir-Ghiasvand, Abbas Nowzari-Dalini, Vida Momenzadeh

Publication date 21 October 2019

Published in Computational \& Mathematical Methods in Medicine (Search for Journal in Brave)

Copyright license Creative Commons Attribution 3.0 Unported

Full work available at URL https://doi.org/10.1155/2014/393908

zbMATH Keywords

\textit{Pin-Align}dynamic programmingprotein-protein interaction networks

Mathematics Subject Classification ID

Dynamic programming (90C39) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Review text

Summary: To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introduce \textit{Pin-Align}, a new tool for local alignment of protein-protein interaction networks. \textit{Pin-Align} accuracy is tested on protein interaction networks from IntAct, DIP, and the Stanford Network Database and the results are compared with other well-known algorithms. It is shown that \textit{Pin-Align} has higher sensitivity and specificity in terms of KEGG Ortholog groups.

Recommendations

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Cites work

• Graph clustering
• scientific article; zbMATH DE number 3231692 (Why is no real title available?)
• Integrated Protein Interaction Networks for 11 Microbes
• Introduction to algorithms.

Cited in

(6)

• Protein mover's distance: a geometric framework for solving global alignment of PPI networks
• The molecular mechanisms associated with PIN7, a protein-protein interaction network of seven pleiotropic proteins
• A heuristic algorithm to align protein interaction networks
• Chapman-Kolmogorov equations for global PPIs with discriminant-EM
• PBNA: an improved probabilistic biological network alignment method
• Exact \(p\)-values for global network alignments via combinatorial analysis of shared GO terms. \textit{REFANGO}: \textit{R}igorous \textit{E}valuation of \textit{F}unctional \textit{A}lignments of \textit{N}etworks using \textit{G}ene \textit{O}ntology

Describes a project that uses

Uses Software

• IsoRankN
• NETAL
• KEGG
• PSI-BLAST
• BLAST
• PathBLAST

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