Abstract
Bacterial lipoproteins play critical roles in various physiological processes including the maintenance of pathogenicity and numbers of them are being considered as potential candidates for generating novel vaccines. In this work, we put forth an algorithm to identify and predict ligand-binding sites in bacterial lipoproteins. The method uses three types of pocket descriptors, namely fpocket descriptors, 3D Zernike descriptors and shell descriptors, and combines them with Support Vector Machine (SVM) method for the classification. The three types of descriptors represent shape-based properties of the pocket as well as its local physio-chemical features. All three types of descriptors, along with their hybrid combinations are evaluated with SVM and to improve classification performance, WEKA-InfoGain feature selection is applied. Results obtained in the study show that the classifier successfully differentiates between ligand-binding and non-binding pockets. For the combination of three types of descriptors, 10 fold cross-validation accuracy of 86.83% is obtained for training while the selected model achieved test Matthews Correlation Coefficient (MCC) of 0.534. Individually or in combination with new and existing methods, our model can be a very useful tool for the prediction of potential ligand-binding sites in bacterial lipoproteins.
Keywords: Bacterial lipoproteins, feature selection, ligand-binding sites, pocket descriptors, prediction, support vector Machine (SVM)
Call for Papers in Thematic Issues
Advancing the Understanding of Regulatory Mechanisms and Diseases Through Biochemistry and Structural Biology
Modern research is increasingly interested in understanding the regulatory mechanisms and diseases through various integrative approaches. Biochemistry and structural biology offer valuable atomic-level insights that help unravel the complexities of cellular regulatory mechanisms and their association with health and disease. The unique advantage of these fields is that they provide ...read more
Protein Based Biomaterials in Environmental Sustainability, Therapy, and Diagnostics
Protein-based biomaterials have wide variety of therapeutic and diagnostic applications. Important properties of these materials are biocompatibility, biodegradability, functional versatility, and ability to interact with life. They are biodegradable so make sought after targets for environmental applications. These materials are also being investigated for increased applications in water filtration technology ...read more
Recent Advances in Protein Engineering and Design
Protein engineering and design have revolutionized biotechnology, medicine, and industrial applications by enabling the creation of novel proteins with tailored functions. Recent advancements in computational modeling, directed evolution, and synthetic biology have expanded the possibilities for engineering proteins with enhanced stability, specificity, and activity. This special issue will explore state-of-the-art ...read more
Therapeutic Proteins and Peptides of Plant Origin
Plants are still the major repository of biologically active substances. In the last two decades, however, natural peptides and proteins of plant origin have gained increasing attention due to their pharmacological activities over a variety of human illnesses, including those mediated by infections and parasitosis and those involving different cellular ...read more
Related Books
Wild Vegetables: Morphology, Phytochemistry and Utility Part 1
Biology for Students
Medicinal Plants of Pilibhit Tiger Reserve (PTR) India
Plant-Microbe Interactions: A Comprehensive Review
Glycosylation and Glycation in Health and Diseases
Phytogenic and Phytochemical as Alternative Feed Additives for Animal Production
Methods and Techniques in Nematology
Mind Maps in Clinical Biochemistry
A Treatise on Ecological Science
From SARS-CoV to MARS-CoV
10
