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Verification of protein structures: Patterns of nonbonded atomic interactions
Open accessAbstract
A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic atomic interactions is described. Different types of atoms are distributed nonrandomly with respect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distributions by statistical methods. Atoms are classified in one of three categories: carbon (C), nitrogen (N), and oxygen (O). This leads to six different combinations of pairwise noncovalently bonded interactions (CC, CN, CO, NN, NO, and OO). A quadratic error function is used to characterize the set of pairwise interactions from nine‐residue sliding windows in a database of 96 reliable protein structures. Regions of candidate protein structures that are mistraced or misregistered can then be identified by analysis of the pattern of nonbonded interactions from each window.
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Cited by
Comparative Protein Structure Modeling of Genes and Genomes
Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.291 · Cited by 3,169
Structure of influenza haemagglutinin at the pH of membrane fusion
Bullough, P. A., Hughson, F. M., Skehel, J. J., & Wiley, D. C. (1994) · Nature · doi:10.1038/371037a0 · Cited by 1,564
Comparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730
Targeting of Ikaros to pericentromeric heterochromatin by direct DNA binding
Cobb, B. S., Morales-Alcelay, S., Kleiger, G., Brown, K. E., Fisher, A. G., & Smale, S. T. (2000) · Genes & Development · doi:10.1101/gad.816400 · Cited by 252
PROKR2 missense mutations associated with Kallmann syndrome impair receptor signalling activity
Monnier, C., Dodé, C., Fabre, L., Teixeira, L., Labesse, G., Pin, J.-P., Hardelin, J.-P., & Rondard, P. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddn318 · Cited by 123
Metadata
- Authors
- Colovos, C., & Yeates, T. O.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 1993-09
- Volume
- 2
- Issue
- 9
- Pages
- 1511-1519
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- OpenAlex
- W2102993309
- Cited by
- 4,498
- References
- 0
- FWCI
- 1.37
- Type
- journal article
- Language
- en
- Open access
- bronze
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