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Local Disordered Region Sampling (LDRS) for Ensemble Modeling of Proteins with Experimentally Undetermined or Low Confidence Prediction Segments
Open accessPreprint — published as 10.1093/bioinformatics/btad739
Abstract
STRUCTURED ABSTRACT: SUMMARY: The Local Disordered Region Sampling (LDRS, pronounced loaders ) tool, developed for the IDPConformerGenerator platform (Teixeira et al . 2022), provides a method for generating all-atom conformations of intrinsically disordered regions (IDRs) at N- and C-termini of and in loops or linkers between folded regions of an existing protein structure. These disordered elements often lead to missing coordinates in experimental structures or low confidence in predicted structures. Requiring only a pre-existing PDB structure of the protein with missing coordinates or with predicted confidence scores and its full-length primary sequence, LDRS will automatically generate physically meaningful conformational ensembles of the missing flexible regions to complete the full-length protein. The capabilities of the LDRS tool of IDPConformerGenerator include modeling phosphorylation sites using enhanced Monte Carlo Side Chain Entropy (MC-SCE) (Bhowmick and Head-Gordon 2015), transmembrane proteins within an all-atom bilayer, and multi-chain complexes. The modeling capacity of LDRS capitalizes on the modularity, ability to be used as a library and via command-line, and computational speed of the IDPConformerGenerator platform. AVAILABILITY AND IMPLEMENTATION: The LDRS module is part of the IDPConformerGenerator modeling suite, which can be downloaded from GitHub at https://github.com/julie-forman-kay-lab/IDPConformerGenerator . IDPConformerGenerator is written in Python and works on Linux, Microsoft Windows, and Mac OS versions that support DSSP. Users can utilize LDRS’s Python API for scripting the same way they can use any part of IDPConformerGenerator’s API, by importing functions from the ‘idpconfgen.ldrs_helper’ library. Otherwise, LDRS can be used as a command line interface application within IDPConformerGenerator. Full documentation is available within the command-line interface (CLI) as well as on IDPConformerGenerator’s official documentation pages ( https://idpconformergenerator.readthedocs.io/en/latest/ ). CONTACT: For support with LDRS please contact Zi Hao (Nemo) Liu via nemo.liu@sickkids.ca or submit an issue in the IDPConformerGenerator repository on GitHub ( https://github.com/julie-forman-kay-lab/IDPConformerGenerator/issues ). SUPPLEMENTARY INFORMATION: The supplementary information document contains, or links to, all the conformer ensembles generated for this publication, the generalized Python scripts using the LDRS Python API, figures of detailed methods, fractional secondary structure information, torsion angle sampling, and the time required to generate the different protein cases.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
AlphaFold and Implications for Intrinsically Disordered Proteins
Ruff, K. M., & Pappu, R. V. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167208 · Cited by 635
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Metadata
- Authors
- Liu, Z. H., Teixeira, J. M. C., Zhang, O., Tsangaris, T. E., Li, J., Gradinaru, C. C., Head-Gordon, T., & Forman-Kay, J. D.
- Affiliations
- University of Toronto (CA)
- Hospital for Sick Children (CA)
- University of California, Berkeley (US)
- Corresponding author
- Forman-Kay, Julie D.
- ORCID
- Venue
- Bioinformatics
- Publisher
- openRxiv
- Published
- 2023-07-27
- Volume
- 39
- Issue
- 12
- ISSN
- 1367-4803 (ISSN-L)
- PMC
- PMC10733734
- OpenAlex
- W4389452578
- Cited by
- 18
- References
- 2
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 4 · 2023: 2
- FWCI
- 1.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by-nc)
- Funders
- Canada Research Chairs
- National Institutes of Health
- Natural Sciences and Engineering Research Council of Canada (-2016-06718, 06718, rgpin-2023-04864)
- National Institute of General Medical Sciences (R01GM127627)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- intrinsically disordered proteins, transmembrane proteins
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