LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design

Authors

  • Cristian R. Munteanu,

    Corresponding author
    1. Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña s/n, 15071 A Coruña, Spain phone: (+34) 981167000, ext. 1302; fax: (+34) 981167160
    • Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña s/n, 15071 A Coruña, Spain phone: (+34) 981167000, ext. 1302; fax: (+34) 981167160

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  • Nieves Pedreira,

    1. Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña s/n, 15071 A Coruña, Spain phone: (+34) 981167000, ext. 1302; fax: (+34) 981167160
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  • Julián Dorado,

    1. Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña s/n, 15071 A Coruña, Spain phone: (+34) 981167000, ext. 1302; fax: (+34) 981167160
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  • Alejandro Pazos,

    1. Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña s/n, 15071 A Coruña, Spain phone: (+34) 981167000, ext. 1302; fax: (+34) 981167160
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  • Lázaro G. Pérez-Montoto,

    1. Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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  • Florencio M. Ubeira,

    1. Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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  • Humberto González-Díaz

    1. Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, 48940, Leioa, Bizkaia, Spain
    2. IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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Abstract

Lectins (Ls) play an important role in many diseases such as different types of cancer, parasitic infections and other diseases. Interestingly, the Protein Data Bank (PDB) contains +3000 protein 3D structures with unknown function. Thus, we can in principle, discover new Ls mining non-annotated structures from PDB or other sources. However, there are no general models to predict new biologically relevant Ls based on 3D chemical structures. We used the MARCH-INSIDE software to calculate the Markov-Shannon 3D electrostatic entropy parameters for the complex networks of protein structure of 2200 different protein 3D structures, including 1200 Ls. We have performed a Linear Discriminant Analysis (LDA) using these parameters as inputs in order to seek a new Quantitative Structure-Activity Relationship (QSAR) model, which is able to discriminate 3D structure of Ls from other proteins. We implemented this predictor in the web server named LECTINPred, freely available at http://bio-aims.udc.es/LECTINPred.php. This web server showed the following goodness-of-fit statistics: Sensitivity=96.7 % (for Ls), Specificity=87.6 % (non-active proteins), and Accuracy=92.5 % (for all proteins), considering altogether both the training and external prediction series. In mode 2, users can carry out an automatic retrieval of protein structures from PDB. We illustrated the use of this server, in operation mode 1, performing a data mining of PDB. We predicted Ls scores for +2000 proteins with unknown function and selected the top-scored ones as possible lectins. In operation mode 2, LECTINPred can also upload 3D structural models generated with structure-prediction tools like LOMETS or PHYRE2. The new Ls are expected to be of relevance as cancer biomarkers or useful in parasite vaccine design.

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