EvoPPI: A Web Application to Compare Protein-Protein Interactions (PPIs) from Different Databases and Species

被引：0

作者：

Vazquez, Noe ^{[1
,2
]}

Rocha, Sara ^{[3
,4
]}

Lopez-Fernandez, Hugo ^{[1
,2
,3
,4
,5
]}

Torres, Andre ^{[3
,4
]}

Camacho, Rui ^{[6
]}

Fdez-Riverola, Florentino ^{[1
,2
,5
]}

Vieira, Jorge ^{[3
,4
]}

Vieira, Cristina P. ^{[3
,4
]}

Reboiro-Jato, Miguel ^{[1
,2
,5
]}

机构：

[1] Univ Vigo, ESEI Escuela Super Ingn Informat, Edificio Politecn,Campus Univ Lagoas S-N, Orense 32004, Spain

[2] Ctr Singular Invest Galicia, Ctr Invest Biomed, Vigo, Spain

[3] Univ Porto, Inst Invest & Inovacao Saude I3S, Rua Alfredo Allen 208, P-4200135 Porto, Portugal

[4] IBMC, Rua Alfredo Allen 208, P-4200135 Porto, Portugal

[5] UVIGO, SERGAS, Galicia Sur Hlth Res Inst IIS Galicia Sur, SING Res Grp, Vigo, Spain

[6] Univ Porto, Fac Engn, DEI, LIAAD, Porto, Portugal

来源：

PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY AND BIOINFORMATICS | 2019年 / 803卷

关键词：

Protein-protein interactions databases; Inter-specific comparisons; Graphical view; DISEASE;

D O I：

10.1007/978-3-319-98702-6_18

中图分类号：

TP18 [人工智能理论];

学科分类号：

081104 ; 0812 ; 0835 ; 1405 ;

摘要：

Biological processes are mediated by protein-protein interactions (PPI) that have been studied using different methodologies, and organized as centralized repositories - PPI databases. The data stored in the different PPI databases only overlaps partially. Moreover, some of the repositories are dedicated to a species or subset of species, not all have the same functionalities, or store data in the same format, making comparisons between different databases difficult to perform. Therefore, here we present EvoPPI (http://evoppi.i3s.up.pt), an open source web application tool that allows users to compare the protein interactions reported in two different interactomes. When interactomes belong to different species, a versatile BLAST search approach is used to identify orthologous/paralogous genes, which to our knowledge is a unique feature of EvoPPI.

引用

页码：149 / 156

页数：8

共 50 条

[31] Application of a chimeric green fluorescent protein to study protein-protein interactions
Garamszegi, N
Garamszegi, ZP
Rogers, MS
DeMarco, SJ
Strehler, EE
BIOTECHNIQUES, 1997, 23 (05) : 864 - +
[32] Update on Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein-Protein Interactions
Fedorov V.A.
Kholina E.G.
Kovalenko I.B.
Gudimchuk N.B.
Orekhov P.S.
Zhmurov A.A.
Supercomputing Frontiers and Innovations, 2020, 7 (04) : 62 - 67
[33] Protein-protein interactions more conserved within species than across species
Mika, Sven
Rost, Burkhard
PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (07) : 698 - 709
[34] Protein-protein interactions: Similar binding sites; Different partners
Keskin, Ozlem
Nussinov, Ruth
BIOPHYSICAL JOURNAL, 2007, : 222A - 222A
[35] Probabilistic prediction of protein-protein interactions from the protein sequences
Chinnasamy, Arunkumar
Mittal, Ankush
Sung, Wing-Kin
COMPUTERS IN BIOLOGY AND MEDICINE, 2006, 36 (10) : 1143 - 1154
[36] Iteratively Predict Protein Functions from Protein-Protein Interactions
Chi, Xiaoxiao
Hou, Jingyu
INFORMATION TECHNOLOGY AND AGRICULTURAL ENGINEERING, 2012, 134 : 771 - 778
[37] Learning to predict protein-protein interactions from protein sequences
Gomez, SM
Noble, WS
Rzhetsky, A
BIOINFORMATICS, 2003, 19 (15) : 1875 - 1881
[38] A CONTINUUM MODEL FOR PROTEIN-PROTEIN INTERACTIONS - APPLICATION TO THE DOCKING PROBLEM
JACKSON, RM
STERNBERG, MJE
JOURNAL OF MOLECULAR BIOLOGY, 1995, 250 (02) : 258 - 275
[39] Application of Machine Learning Approaches for Protein-protein Interactions Prediction
Zhang, Mengying
Su, Qiang
Lu, Yi
Zhao, Manman
Niu, Bing
MEDICINAL CHEMISTRY, 2017, 13 (06) : 506 - 514
[40] Towards the Inhibition of Protein-Protein Interactions (PPIs) in STAT3: Insights into a New Class of Benzothiadiazole Derivatives
Mori, Matteo
Gilardoni, Ettore
Regazzoni, Luca
Pedretti, Alessandro
Colombo, Diego
Parkinson, Gary
Asai, Akira
Meneghetti, Fiorella
Villa, Stefania
Gelain, Arianna
MOLECULES, 2020, 25 (15):

← 1 2 3 4 5 →