ArticleFrontiers in chemistry2024
Prostruc: an open-source tool for 3D structure prediction using homology modeling.
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 5 papers.
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Who cites it
5 citing papers in PubMed.
- MARVpred: machine learning prediction of inhibitors targeting Marburg virus Gene 4 Small ORF protein.BMC infectious diseases · 2026Article
- Efficient and easy gene expression and genetic variation data analysis and visualization using exvar.Scientific reports · 2025Article
- TargetingFrontiers in bioinformatics · 2025Article
- Enhanced deep Convolutional Neural Network for SARS-CoV-2 variants classification.Frontiers in artificial intelligence · 2025Article
- Machine learning and molecular docking prediction of potential inhibitors against dengue virus.Frontiers in chemistry · 2024Article
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Authors and funding
7 authors.
Funding
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Abstract
Introduction: Homology modeling is a widely used computational technique for predicting the three-dimensional (3D) structures of proteins based on known templates,evolutionary relationships to provide structural insights critical for understanding protein function, interactions, and potential therapeutic targets. However, existing tools often require significant expertise and computational resources, presenting a barrier for many researchers. Methods: Prostruc is a Python-based homology modeling tool designed to simplify protein structure prediction through an intuitive, automated pipeline. Integrating Biopython for sequence alignment, BLAST for template identification, and ProMod3 for structure generation, Prostruc streamlines complex workflows into a user-friendly interface. The tool enables researchers to input protein sequences, identify homologous templates from databases such as the Protein Data Bank (PDB), and generate high-quality 3D structures with minimal computational expertise. Prostruc implements a two-stage vSquarealidation process: first, it uses TM-align for structural comparison, assessing Root Mean Deviations (RMSD) and TM scores against reference models. Second, it evaluates model quality via QMEANDisCo to ensure high accuracy. Results: The top five models are selected based on these metrics and provided to the user. Prostruc stands out by offering scalability, flexibility, and ease of use. It is accessible via a cloud-based web interface or as a Python package for local use, ensuring adaptability across research environments. Benchmarking against existing tools like SWISS-MODEL,I-TASSER and Phyre2 demonstrates Prostruc's competitive performance in terms of structural accuracy and job runtime, while its open-source nature encourages community-driven innovation. Discussion: Prostruc is positioned as a significant advancement in homology modeling, making high-quality protein structure prediction more accessible to the scientific community.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.