TY - GEN
T1 - ProtRet
T2 - 13th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2019
AU - Zaki, Nazar
AU - Al Yammahi, Maryam
AU - Habuza, Tetiana
N1 - Funding Information:
Acknowledgments. The authors acknowledge financial support from the ICT Fund (Grant # G00001472) and the UAEU (Grant # G00002659).
Funding Information:
The authors acknowledge financial support from the ICT Fund (Grant # G00001472) and the UAEU (Grant # G00002659).
Publisher Copyright:
© 2020, Springer Nature Switzerland AG.
PY - 2020
Y1 - 2020
N2 - The identification of protein complexes is becoming increasingly important to our understanding of cellular functionality. However, if a biologist wishes to investigate a certain protein, currently no method exists to assist him/her to accurately retrieve the possible protein partners that are expected to be in the same functional complex. Here, we introduce ProtRet, a web server that functions as an interface for an improved Pigeonhole approach to identify protein complexes in protein-protein interaction networks. The approach provides high-quality protein comparison that is particularly valuable because of its accurate statistical estimates based on fuzzy criterion and Hamming distance. The proposed method was tested on two high-throughput experimental protein-protein interaction data sets and two gold standard data sets and was able to retrieve more correct protein members than all existing methods. The web server is accessible from the link http://www.protret.com/.
AB - The identification of protein complexes is becoming increasingly important to our understanding of cellular functionality. However, if a biologist wishes to investigate a certain protein, currently no method exists to assist him/her to accurately retrieve the possible protein partners that are expected to be in the same functional complex. Here, we introduce ProtRet, a web server that functions as an interface for an improved Pigeonhole approach to identify protein complexes in protein-protein interaction networks. The approach provides high-quality protein comparison that is particularly valuable because of its accurate statistical estimates based on fuzzy criterion and Hamming distance. The proposed method was tested on two high-throughput experimental protein-protein interaction data sets and two gold standard data sets and was able to retrieve more correct protein members than all existing methods. The web server is accessible from the link http://www.protret.com/.
KW - Information retrieval
KW - Pigeonhole method
KW - Protein complexes
KW - Protein-protein interaction
UR - http://www.scopus.com/inward/record.url?scp=85068616093&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85068616093&partnerID=8YFLogxK
U2 - 10.1007/978-3-030-23873-5_1
DO - 10.1007/978-3-030-23873-5_1
M3 - Conference contribution
AN - SCOPUS:85068616093
SN - 9783030238728
T3 - Advances in Intelligent Systems and Computing
SP - 1
EP - 7
BT - Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, PACBB 2019
A2 - Fdez-Riverola, Florentino
A2 - Rocha, Miguel
A2 - Mohamad, Mohd Saberi
A2 - Zaki, Nazar
A2 - Castellanos-Garzón, José A.
PB - Springer Verlag
Y2 - 26 June 2019 through 28 June 2019
ER -