ArticlePeerJ2014
FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models.
Article in PeerJ, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Polycationic Peptides That Bind T-Box Riboswitch Antiterminator RNA and Inhibit Riboswitch Function.Chemical biology & drug design · 2026Article
- Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering.Journal of chemical information and modeling · 2024Article
- PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling.BMC bioinformatics · 2022Article
- Article
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Authors and funding
3 authors.
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Abstract
We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.
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Registered trials
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