ArticleScientific reports2025
A comparative study of computational modeling approaches for evaluating structural dynamics and algorithmic suitability of short length peptides.
Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Molecular Dynamics Simulation and MM/PBSA Analysis of α-Mangostin Stabilization in SoluplusInternational journal of molecular sciences · 2026Article
- Reversing the Fold: Polyanionic Macrocycle Dissolves αA66-80 Crystallin Peptide Aggregates.Biomacromolecules · 2026Article
- Integrative subtractive genomics and molecular dynamics-based approach for drug repurposing against female genital tuberculosis.Molecular diversity · 2026Article
- Artificial Intelligence-Driven Discovery and Optimization of Antimicrobial Peptides Targeting ESKAPE Pathogens and Multidrug-Resistant Fungi.Microorganisms · 2026Review
- Beyond antibiotics: artificial intelligence-enabled anti-infective ecosystems for next-generation precision therapeutics against antimicrobial resistance.Frontiers in cellular and infection microbiology · 2026Article
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Abstract
The existing protein or peptide modeling algorithms are insufficient for accurately modeling short peptides, which are highly unstable in nature. Thus, there is a need to identify their strengths and weaknesses. Hence, we have performed modeling of a random set of peptides using four different algorithms, namely, AlphaFold, PEP-FOLD, Threading and Homology Modeling. The structures were analyzed using Ramachandran plot, VADAR, and molecular dynamics (MD) simulation. The results were correlated with their physicochemical properties and sequence characteristics. Our study reveals novel insights about strengths of each of the modeling algorithms. We found that AlphaFold and Threading complement each other in case of more hydrophobic peptides. Similarly, PEP-FOLD and Homology Modeling complement each other when modeling more hydrophilic peptides. We also found that PEP-FOLD gives both compact structure and stable dynamics for most of the peptides, whereas AlphaFold gives a compact structure for most of these. Finally, our study points towards the usage of integrated approaches in future, thereby, combining the strengths of different modeling algorithms.
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