Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F15%3A00081013" target="_blank" >RIV/00216224:14740/15:00081013 - isvavai.cz</a>
Result on the web
<a href="http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00159" target="_blank" >http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00159</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.5b00159" target="_blank" >10.1021/acs.jctc.5b00159</a>

Result language
angličtina
Original language name
Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes
Original language description
Protein carbohydrate recognition is crucial in many vital biological processes including host-pathogen recognition, cell-signaling, and catalysis. Accordingly, computational prediction of protein-carbohydrate binding free energies is of enormous interestfor drug design. However, the accuracy of current force fields (FFs) for predicting binding free energies of protein-carbohydrate complexes is not well understood owing to technical challenges such as the highly polar nature of the complexes, anomerization, and conformational flexibility of carbohydrates. The present study evaluated the performance of alchemical predictions of binding free energies with the GAFF1.7/AM1-BCC and GLYCAMO6j force fields for modeling protein carbohydrate complexes. Mean unsigned errors of 1.1 +/- 0.06 (GLYCAMO6j) and 2.6 +/- 0.08 (GAFF1.7/AM1-BCC) kcal.mol(-1) are achieved for a large data set of monosaccharide ligands for Ralstonia solanacearum lectin (RSL).
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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