The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Crystal contacts as nature's docking solutions
Abstract
The assumption that crystal contacts reflect natural macromolecular interactions makes a basis for many studies in structural biology. However, the crystal state may correspond to a global minimum of free energy where biologically relevant interactions are sacrificed in favor to unspecific contacts. A large‐scale docking experiment was performed to assess the extent of misrepresentation of natural (in‐solvent) protein dimers by crystal packing. As found, the failure rate of docking may be quantitatively interpreted if both calculation errors and misrepresentation effects are taken into account. The failure rate analysis is based on the assumption that crystal structures reflect thermodynamic equilibrium between different dimeric configurations. The analysis gives an estimate of misrepresentation probability, which suggests that weakly bound complexes with KD ≥ 100 μM (some 20% of all dimers in the PDB) have higher than 50% chances to be misrepresented by crystals. The developed theoretical framework is applicable in other studies, where experimental results may be viewed as snapshots of systems in thermodynamic equilibrium. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010
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
Principles of protein-protein interactions
Jones, S., & Thornton, J. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.13 · Cited by 2,684
ZDOCK: An initial‐stage protein‐docking algorithm
Chen, R., Li, L., & Weng, Z. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10389 · Cited by 1,393
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
CAPRI: A Critical Assessment of PRedicted Interactions
Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J. E., Vajda, S., Vakser, I., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10381 · Cited by 703
Folding funnels, binding funnels, and protein function
Tsai, C., Kumar, S., Ma, B., & Nussinov, R. (1999) · Protein Science · doi:10.1110/ps.8.6.1181 · Cited by 648
Folding funnels and binding mechanisms
Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.9.713 · Cited by 594
Cited by
Alpha-Synuclein defects autophagy by impairing SNAP29-mediated autophagosome-lysosome fusion
Tang, Q., Gao, P., Arzberger, T., Höllerhage, M., Herms, J., Höglinger, G., & Koeglsperger, T. (2021) · Cell Death & Disease · doi:10.1038/s41419-021-04138-0 · Cited by 103
Antiviral signalling by a cyclic nucleotide activated CRISPR protease
Rouillon, C., Schneberger, N., Chi, H., Blumenstock, K., Da Vela, S., Ackermann, K., Moecking, J., Peter, M. F., Boenigk, W., Seifert, R., et al. (2023) · Nature · doi:10.1038/s41586-022-05571-7 · Cited by 66
Kumar, N., Kaushik, R., Zhang, K. Y. J., Uversky, V. N., Sahu, U., Sood, R., & Bhatia, S. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26467 · Cited by 15
The 2.3 Å Structure of A21, a Protein Component of the Conserved Poxvirus Entry-Fusion Complex
Diesterbeck, U. S., Muslinkina, L. A., Gittis, A. G., Singh, K., Moss, B., & Garboczi, D. N. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169097 · Cited by 9
Metadata
- Authors
- Krissinel, E.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2009-05-06
- Volume
- 31
- Issue
- 1
- Pages
- 133-143
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2095521702
- Cited by
- 365
- References
- 6
- FWCI
- 6.22
- 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
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.
