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| On the hydrophobicity of peptides: Comparing empirical predictions of peptide log P values |
Authors | Sarah J. Thompson1,2, Channa K. Hattotuwagama1, John D. Holliday 2 and Darren R. Flower 1* | |
Affiliation | 1 Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK; 2 Dept. of Information Studies, University of Sheffield
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| darren.flower@jenner.ac.uk; *Corresponding author
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Phone | +44 1635 577954
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Fax | +44 1635 577908
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Article Type | Prediction Model
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Date | received October 14, 2006; accepted November 02, 2006; published online November 14, 2006
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Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient logP, is useful for the development of predictive Quantitative Structure-Activity Relationships (QSARs). We have investigated the accuracy of available programs for the prediction of logP values for peptides with known experimental values obtained from the literature. Eight prediction programs were tested, of which seven programs were fragment-based methods: XLogP, LogKow, PLogP, ACDLogP, AlogP, Interactive Analysis�s LogP and MlogP; and one program used a whole molecule approach: QikProp. The predictive accuracy of the programs was assessed using r2 values, with ALogP being the most effective (r2 = 0.822) and MLogP the least (r2 = 0.090). We also examined three distinct types of peptide structure: blocked, unblocked, and cyclic. For each study (all peptides, blocked, unblocked and cyclic peptides) the performance of programs rated from best to worse is as follows: all peptides � ALogP, QikProp, PLogP, XLogP, IALogP, LogKow, ACDLogP, and MlogP; blocked peptides � PLogP, XLogP, ACDLogP, IALogP, LogKow, QikProp, ALogP, and MLogP; unblocked peptides � QikProp, IALogP, ALogP, ACDLogP, MLogP, XLogP, LogKow and PLogP; cyclic peptides � LogKow, ALogP, XLogP, MLogP, QikProp, ACDLogP, IALogP. In summary, all programs gave better predictions for blocked peptides, while, in general, logP values for cyclic peptides were under-predicted and those of unblocked peptides were over-predicted.
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Keywords
| partition coefficient; logP; peptides; octanol; biphasic system; QSAR | |
Citation | Thompson et al., Bioinformation 1(7): 237-241 (2006) | |
Edited by | P. Kangueane
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ISSN | 0973-2063
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Publisher |
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Copyright | Publisher
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Copyright Transfer Statement | The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes. | |
License | This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
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