ProtDCal‐Suite: A web server for the numerical codification and functional analysis of proteins

Computational tools for the analysis of protein data and the prediction of biological properties are essential in life sciences and biomedical research. Here, we introduce ProtDCal‐Suite, a web server comprising a set of machine learning‐based methods for studying proteins. The main module of ProtDC...

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Bibliographic Details
Published in:Protein science 2019-09, Vol.28 (9), p.1734-1743
Main Authors: Romero‐Molina, Sandra, Ruiz‐Blanco, Yasser B., Green, James R., Sanchez‐Garcia, Elsa
Format: Article
Language:English
Subjects:
Amino acids
Biological properties
Codification
Computational Biology - methods
Computer applications
Databases, Protein
descriptor
Entropy (Information theory)
enzymes
Functional analysis
Glycosylation
Internet
Learning algorithms
Machine Learning
Models, Molecular
Modules
N‐glycosylation
Predictions
Proteins
Proteins - chemistry
Proteins - metabolism
protein–protein interactions
Servers
Software
Tools for Protein Science
web server
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Summary:Computational tools for the analysis of protein data and the prediction of biological properties are essential in life sciences and biomedical research. Here, we introduce ProtDCal‐Suite, a web server comprising a set of machine learning‐based methods for studying proteins. The main module of ProtDCal‐Suite is the ProtDCal software. ProtDCal translates the structural information of proteins into numerical descriptors that serve as input to machine‐learning techniques. The ProtDCal‐Suite server also incorporates a post‐processing optional stage that allows ranking and filtering the obtained descriptors by computing their Shannon entropy values across the input set of proteins. ProtDCal's codification was used in the development of models for the prediction of specific protein properties. Thus, the other modules of ProtDCal‐Suite are protein analysis tools implemented using ProtDCal's descriptors. Among them are PPI‐Detect, for predicting the interaction likelihood of protein–protein and protein–peptide pairs, Enzyme Identifier, for identifying enzymes from amino acid sequences or 3D structures, and Pred‐NGlyco, for predicting N‐glycosylation sites. ProtDCal‐Suite is freely accessible at https://protdcal.zmb.uni‐due.de.
ISSN:0961-8368
1469-896X
DOI:10.1002/pro.3673