A method for predicting linear and conformational B-cell epitopes in an antigen from its primary sequence

Abstract

B-cell is an essential component of the immune system that plays a vital role in providing the immune response against any pathogenic infection by producing antibodies. Existing methods either predict linear or conformational B-cell epitopes in an antigen. In this study, a single method was developed for predicting both types (linear/conformational) of B-cell epitopes. The dataset used in this study contains 3875 B-cell epitopes and 3996 non-B-cell epitopes, where B-cell epitopes consist of both linear and conformational B-cell epitopes. Our primary analysis indicates that certain residues (like Asp, Glu, Lys, Asn) are more prominent in B-cell epitopes. We developed machine-learning based methods using different types of sequence composition and achieved the highest AUC of 0.80 using dipeptide composition. In addition, models were developed on selected features, but no further improvement was observed. Our similarity-based method implemented using BLAST shows a high probability of correct prediction with poor sensitivity. Finally, we came up with a hybrid model that combine alignment free (dipeptide based random forest model) and alignment-based (BLAST based similarity) model. Our hybrid model attained maximum AUC 0.83 with MCC 0.49 on the independent dataset. Our hybrid model performs better than existing methods on an independent dataset used in this study. All models trained and tested on 80% data using cross-validation technique and final model was evaluated on 20% data called independent or validation dataset. A webserver and standalone package named "CLBTope" has been developed for predicting, designing, and scanning B-cell epitopes in an antigen sequence (https://webs.iiitd.edu.in/raghava/clbtope/).

Thiosemicarbazone ligands based transition metal complexes: A multifaceted investigation of antituberculosis, anti‐inflammatory, antibacterial, antifungal activities, and molecular docking, density functional theory, molecular electrostatic potential, absorption, distribution, metabolism, excretion, and toxicity studies

“…Following this incubation, 25 μL of Alamar Blue and a 10%-80% Tween solution were added to the aforementioned sterile 96-well plate, and it was returned to the incubator for an additional 1 day. 15 The minimum inhibitory concentration (MIC) values were determined by examining the growth of mycobacterium, indicated by a pink coloration in the well, while the absence of bacterial growth was indicated by a blue coloration.…”

“…The highly potent compounds (2), ( 7), ( 8), (9), and (10) underwent comprehensive molecular docking investigations to understand their interactions with two pivotal proteins: M. tuberculosis phosphatidylinositol phosphate synthase (PDB ID: 6H53), 18 relevant to TB, and cyclooxygenase-2 (COX-2, prostaglandin synthase-2) complexed with a selective inhibitor (PDB ID: 1CX2), 19 pertinent to inflammatory conditions. To conduct these intricate docking experiments, AutoDock software, 15 a widely recognized and trusted tool in the field, was employed. A critical aspect of the docking strategy was the choice of blind docking.…”

“…For ligands, (2) (HL 2 ) (0.118 ± 0.007 μmol/mL) demonstrates a superior anti-TB effect compared with (1) (HL 1 ), attributable to the influence of electron-withdrawing groups of the moiety. 15,31,32 Thus, the ligand (2) and its complexes have more potency to inhibit the growth of TB infection compared with the ligand (1) and its complexes. 2.…”

Exploring the antimicrobial, antioxidant and cytotoxic activities of organyltellurium (IV) complexes incorporating 2‐hydroxy‐1‐naphthaldehyde schiff base ligand: Synthesis, spectroscopic investigations and theoretical studies

“…The antioxidant properties of the Schiff base (HNDP) and its complexes (5a-5f), as well as the standard ascorbic acid were evaluated using the DPPH assay procedure. 54,55 In this procedure, the solution mixtures comprised 1 ml of the test samples diluted to various concentrations (20,40,60,80, 100 μg/ml) and 1 ml of 0.3 mM DPPH, pre-dissolved in DMSO. The solution mixture was then left in a dark place at an ambient temperature for half hour.…”

“…We assessed the structure-activity relationship to understand the impact of the synthesized compounds on pharmacological activity (supplementary Figure S29). Literature study [35][36][37][38]40,80 revealed that the attached groups of the moiety significantly affect the antimicrobial, antioxidant and anti-cancer activities. Therefore, we synthesized various group based organyltellurium complexes for comparing their pharmacological activities.…”