The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Sub-angstrom modeling of complexes between flexible peptides and globular proteins: Sub-Angstrom Modeling of Flexible Peptides
Abstract
A wide range of regulatory processes in the cell are mediated by flexible peptides that fold upon binding to globular proteins. Computational efforts to model these interactions are hindered by the large number of rotatable bonds in flexible peptides relative to typical ligand molecules, and the fact that different peptides assume different backbone conformations within the same binding site. In this study, we present Rosetta FlexPepDock, a novel tool for refining coarse peptide-protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark that is based on a large nonredundant dataset of 89 peptide-protein interactions. Importantly, side chains of known binding motifs are modeled particularly well, typically with atomic accuracy. In addition, our protocol has improved modeling quality for the important application of cross docking to PDZ domains. We anticipate that the ability to create high resolution models for a wide range of peptide-protein complexes will have significant impact on structure-based functional characterization, controlled manipulation of peptide interactions, and on peptide-based drug design.
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Cites
Intrinsically unstructured proteins and their functions
Dyson, H. J., & Wright, P. E. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1589 · Cited by 3,871
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Recognition of Unique Carboxyl-Terminal Motifs by Distinct PDZ Domains
Songyang, Z., Fanning, A. S., Fu, C., Xu, J., Marfatia, S. M., Chishti, A. H., Crompton, A., Chan, A. C., Anderson, J. M., & Cantley, L. C. (1997) · Science · doi:10.1126/science.275.5296.73 · Cited by 1,385
Coupling of folding and binding for unstructured proteins
Dyson, H. J., & Wright, P. E. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00289-0 · Cited by 1,327
Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks
Neduva, V., Linding, R., Su-Angrand, I., Stark, A., Masi, F. D., Gibson, T. J., Lewis, J., Serrano, L., & Russell, R. B. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030405 · Cited by 359
Structure and function of the WW domain
Sudol, M. (1996) · Progress in Biophysics and Molecular Biology · doi:10.1016/s0079-6107(96)00008-9 · Cited by 296
Protein structure prediction: when is it useful?
Zhang, Y. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.02.005 · Cited by 277
Cited by
Improved Docking of Polypeptides with Glide
Tubert-Brohman, I., Sherman, W., Repasky, M., & Beuming, T. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400128m · Cited by 1,308
Harnessing protein folding neural networks for peptide–protein docking
Tsaban, T., Varga, J. K., Avraham, O., Ben-Aharon, Z., Khramushin, A., & Schueler-Furman, O. (2022) · Nature Communications · doi:10.1038/s41467-021-27838-9 · Cited by 1,205
Self-citationMacromolecular modeling and design in Rosetta: recent methods and frameworks
Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0848-2 · Cited by 888
Self-citationOvercoming the Reticuloendothelial System Barrier to Drug Delivery with a “Don’t-Eat-Us” Strategy
Tang, Y., Wang, X., Li, J., Nie, Y., Liao, G., Yu, Y., & Li, C. (2019) · ACS Nano · doi:10.1021/acsnano.9b05679 · Cited by 339
Chen, S., Lin, T., Basu, R., Ritchey, J., Wang, S., Luo, Y., Li, X., Pei, D., Kara, L. B., & Cheng, X. (2024) · Nature Communications · doi:10.1038/s41467-024-45766-2 · Cited by 324
Metadata
- Authors
- Raveh, B., London, N., & Schueler-Furman, O.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2010-03-18
- Volume
- 78
- Issue
- 9
- Pages
- 2029-2040
- ISSN
- 0887-3585 (ISSN-L)
- OpenAlex
- W2116890528
- Cited by
- 430
- References
- 7
- FWCI
- 6.03
- Type
- journal article
- Language
- en
- Open access
- closed
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