Prostruc: an open-source tool for 3D structure prediction using homology modeling

• Published in: Frontiers in chemistry 2024, Vol.12, p.1509407
• Main Authors: Pawar, Shivani V, Banini, Wilson Sena Kwaku, Shamsuddeen, Musa Muhammad, Jumah, Toheeb A, Dolling, Nigel N O, Tiamiyu, Abdulwasiu, Awe, Olaitan I
• Format: Article
• Language: English
• Subjects: biopython; BLAST; Chemistry; homology modeling; open-source software; ProMod3; protein structure prediction
• ISSN: 2296-2646; 2296-2646
• DOI: 10.3389/fchem.2024.1509407

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. 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. 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. Prostruc is positioned as a significant advancement in homology modeling, making high-quality protein structure prediction more accessible to the scientific community.