ArticleFrontiers in chemistry2024
Computational modeling of cyclotides as antimicrobial agents against
Article in Frontiers in chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Design of a cyclic peptide targeting intracellular Staphylococcus aureus.Molecular biomedicine · 2026Article
- Multi-Target Bioactivity ofPharmaceuticals (Basel, Switzerland) · 2026Article
- Chalcone-sulfonate ester derivatives as dual urease and α-amylase inhibitors: synthesis, biological evaluation and integrated computational studies.RSC advances · 2026Article
- Integrated UHPLC-QTOF-MSJournal of computer-aided molecular design · 2026Article
- Identification of natural FGFR3 inhibitor for glioma using integrated computational and microRNA regulatory analysis.Scientific reports · 2026Article
- Computational screening of AI-derived cyclotides as putative VEGFR2 binders for wound-site angiogenesis.Scientific reports · 2026Article
- AI fragmentation-based optimization of Sorafenib derivatives targeting VEGFR2 for angiogenesis-related pathologies: a structure-based in-silico study.Scientific reports · 2026Article
- Computational prediction of cyclotides from Viola odorata as potential inhibitors against the neuraminidase of Streptococcus pneumoniae.Molecular diversity · 2026Article
- Article
- AI-assisted identification of innovative phytochemicals from Aizoon canariense aimed at brachyury protein in chordoma: a computational strategy.Scientific reports · 2025Article
- In silico investigation of ketamine and methylphenidate drug-drug conjugate for MDD and ADHD treatment using MD simulations and MMGBSA.Scientific reports · 2025Article
- Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach.Journal, genetic engineering & biotechnology · 2025Article
- Evaluation of silvestrol as a potential therapeutic agent for pediatric COVID-19: an interpreted computational and phytochemistry approach.Frontiers in pharmacology · 2025Article
- An integrated mutation-based immunoinformatic approach incorporating variability in epitopes: a study based on HIV subtype C.Frontiers in immunology · 2025Article
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Authors and funding
6 authors.
Funding
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Abstract
Background: Methodology: The PorB Porin protein was retrieved from the Protein Data Bank (PDB ID: 4AUI), cleaned, and visualized using Discovery Visual Studio. Physicochemical properties were predicted using ProtParam. Cyclotides were obtained from the CyBase database, with 3D models generated and refined via the Swiss Model for docking studies. HDOCK was used for molecular docking. Toxicity and allergenicity predictions were performed with ToxinPred and AlgPred. A heatmap of the peptide was created using Protein-Sol. Molecular dynamics (MD) simulations were conducted for 100,000 picoseconds using Desmond from Schrödinger LLC, while binding energy was analyzed using MMGBSA. Immune response simulations were done with C-ImmSim 10.1, and peptide simulation in water was performed via WebGro. Results: The protein's GRAVY value is -0.539, indicating moderate hydrophilicity, and its isoelectric point is 9.14, suggesting a fundamental nature. Globa D had the highest docking score (-270.04 kcal/mol) and was deemed non-toxic and non-allergenic. MD simulations showed stable protein-ligand interactions, and MMGBSA revealed a low binding energy of -36.737 kcal/mol. Immune simulations indicated an effective immune response and peptide simulations demonstrated Globa D's stability in water, making it a potential candidate for pharmaceutical applications. Conclusion: Globa D proved the best drug candidate against
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