The DOI matches its Crossref record.
Conformations of folded proteins in restricted spaces
Abstract
A new method is presented to examine the complete range of folded topologies accessible in the compact state of globular proteins. The procedure is to generate all conformations, with volume exclusion, upon a lattice in a space restricted to the individual protein's known compact conformational space. Using one lattice point per residue, we find 10(2)-10(4) possible compact conformations for the five small globular proteins studied. Subsequently, these conformations are evaluated in terms of residue-specific, pairwise contact energies that favor nonbonded, hydrophobic interactions. Native structures for the five proteins are always found within the best 2% of all conformers generated. This novel method is simple and general and can be used to determine a small group of most favorable overall arrangements for the folding of specific amino acid sequences within a restricted space.
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
Cited by
Funnels, pathways, and the energy landscape of protein folding: A synthesis
Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340210302 · Cited by 2,648
“Work on realistic lattice models for small proteins confined to their proper shape (where complete enumeration can be carried out) suggests the possibility of deep low energy structures that are globally different in form [56, 57].”
BackgroundTHEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
Onuchic, J. N., Luthey-Schulten, Z., & Wolynes, P. G. (1997) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.48.1.545 · Cited by 2,210
Principles of protein folding — A perspective from simple exact models
Dill, K. A., Bromberg, S., Yue, K., Chan, H. S., Fiebig, K. M., Yee, D. P., & Thomas, P. D. (1995) · Protein Science · doi:10.1002/pro.5560040401 · Cited by 1,525
Miyazawa, S., & Jernigan, R. L. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0114 · Cited by 1,230
Self-citationBiomolecular Modeling: Goals, Problems, Perspectives
van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D. P., Glättli, A., Hünenberger, P. H., et al. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200502655 · Cited by 561
Metadata
- Authors
- Covell, D. G., & Jernigan, R. L.
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1990-04
- Volume
- 29
- Issue
- 13
- Pages
- 3287-3294
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2028099075
- Cited by
- 227
- References
- 0
- FWCI
- 5.81
- Type
- journal article
- Language
- en
- Open access
- closed
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: Conformations of folded proteins in restricted spaces. https://app.cochat.ai/papers/10.1021/bi00465a020
- The paper
- Covell, D. G., & Jernigan, R. L. (1990). Conformations of folded proteins in restricted spaces. Biochemistry. https://doi.org/10.1021/bi00465a020
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.
