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Very fast empirical prediction and rationalization of protein pKa values
Abstract
A very fast empirical method is presented for structure‐based protein pK a prediction and rationalization. The desolvation effects and intra‐protein interactions, which cause variations in pK a values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pK a sites. A computer program is written to automatically predict pK a values based on these empirical relationships within a couple of seconds. Unusual pK a values at buried active sites, which are among the most interesting protein pK a values, are predicted very well with the empirical method. A test on 233 carboxyl, 12 cysteine, 45 histidine, and 24 lysine pK a values in various proteins shows a root‐mean‐square deviation (RMSD) of 0.89 from experimental values. Removal of the 29 pK a values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pK a values. Proteins 2005. © 2005 Wiley‐Liss, Inc.
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Metadata
- Authors
- Li, H., Robertson, A. D., & Jensen, J. H.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2005-11-17
- Volume
- 61
- Issue
- 4
- Pages
- 704-721
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2152997175
- Cited by
- 2,054
- References
- 0
- FWCI
- 15.44
- Type
- journal article
- Language
- en
- Open access
- closed
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