The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
Multipass membrane protein structure prediction using Rosetta
Open accessAbstract
We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures. The membrane environment is modeled by embedding the protein chain into a model membrane represented by parallel planes defining hydrophobic, interface, and polar membrane layers for each energy evaluation. The optimal embedding is determined by maximizing the exposure of surface hydrophobic residues within the membrane and minimizing hydrophobic exposure outside of the membrane. Protein conformations are built up using the Rosetta fragment assembly method and evaluated using a new membrane‐specific version of the Rosetta low‐resolution energy function in which residue–residue and residue–environment interactions are functions of the membrane layer in addition to amino acid identity, distance, and density. We find that lower energy and more native‐like structures are achieved by sequential addition of helices to a growing chain, which may mimic some aspects of helical protein biogenesis after translocation, rather than folding the whole chain simultaneously as in the Rosetta soluble protein prediction method. In tests on 12 membrane proteins for which the structure is known, between 51 and 145 residues were predicted with root‐mean‐square deviation <4 Å from the native structure. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4315 · Cited by 12,654
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor
Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Trong, I. L., Teller, D. C., Okada, T., Stenkamp, R. E., et al. (2000) · Science · doi:10.1126/science.289.5480.739 · Cited by 5,637
Jones, D. T. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3091 · Cited by 5,449
The PSIPRED protein structure prediction server
McGuffin, L. J., Bryson, K., & Jones, D. T. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.4.404 · Cited by 3,838
Hopkins, A. L., & Groom, C. R. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd892 · Cited by 3,305
A hidden Markov model for predicting transmembrane helices in protein sequences.
Sonnhammer, E. L. L., von HEIJNE, G., & Krogh, A. (1998) · PubMed · Cited by 2,505
Tmbase-A database of membrane spanning protein segments
Hofmann, K., & Stoffel, W. (1993) · Medical Entomology and Zoology · Cited by 2,240
The HMMTOP transmembrane topology prediction server
Tusnády, G. E., & Simon, I. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.9.849 · Cited by 1,907
MEMBRANE PROTEIN FOLDING AND STABILITY: Physical Principles
White, S. H., & Wimley, W. C. (1999) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.28.1.319 · Cited by 1,764
Cited by
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., et al. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00125 · Cited by 1,532
Self-citationThe second wave of synthetic biology: from modules to systems
Purnick, P. E. M., & Weiss, R. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2698 · Cited by 1,181
Macromolecular 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-citationVoltage-gated ion channels and gating modifier toxins
Catterall, W. A., Cestèle, S., Yarov-Yarovoy, V., Yu, F. H., Konoki, K., & Scheuer, T. (2007) · Toxicon · doi:10.1016/j.toxicon.2006.09.022 · Cited by 640
Self-citationThree-Dimensional Structures of Membrane Proteins from Genomic Sequencing
Hopf, T. A., Colwell, L. J., Sheridan, R., Rost, B., Sander, C., & Marks, D. S. (2012) · Cell · doi:10.1016/j.cell.2012.04.012 · Cited by 512
Metadata
- Authors
- Yarov‐Yarovoy, V., Schonbrun, J., & Baker, D.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2005-12-21
- Volume
- 62
- Issue
- 4
- Pages
- 1010-1025
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2101810621
- Cited by
- 323
- References
- 60
- FWCI
- 4.61
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Multipass membrane protein structure prediction using Rosetta. https://app.cochat.ai/papers/10.1002/prot.20817
- The paper
- Yarov‐Yarovoy, V., Schonbrun, J., & Baker, D. (2006). Multipass membrane protein structure prediction using Rosetta. Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/prot.20817
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
