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231225s2017 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.24845
|2 doi
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|a pubmed24n0911.xml
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|a DE-627
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|a eng
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| 100 |
1 |
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|a Huang, Ming
|e verfasserin
|4 aut
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| 245 |
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|a Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse-grained molecular dynamics simulations with a weighted histogram analysis method
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|c 2017
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
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|2 rdacarrier
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|a Date Revised 20.11.2019
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|a published: Print-Electronic
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|a Citation Status PubMed-not-MEDLINE
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|a © 2017 Wiley Periodicals, Inc.
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|a We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with the weighted histogram analysis method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse-grained (CG) force field (MARTINI) is less prone to significant error induced by inadequate-sampling than using an atomistic force field (AMBER). We further demonstrate that using CG MD to pull 3-4 residue peptide segments while leaving the remaining peptide segments in the binding groove and adding up the binding free energies of all peptide segments gives robust binding free energy estimations, which are in good agreement with the experimentally measured binding affinities for the peptide sequences studied. Our approach thus provides a promising and computationally efficient way to rapidly and reliably estimate the binding free energy between an arbitrary peptide and an MHC class II molecule. © 2017 Wiley Periodicals, Inc
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|a Journal Article
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|a Research Support, Non-U.S. Gov't
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|a MHC
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|a binding free energy
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|a coarse-grained
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|a peptide
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|a peptide-MHC binding affinity
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| 650 |
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|a umbrella sampling method
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| 700 |
1 |
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|a Huang, Wenjun
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Wen, Fei
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Larson, Ronald G
|e verfasserin
|4 aut
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| 773 |
0 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 38(2017), 23 vom: 05. Sept., Seite 2007-2019
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
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|g volume:38
|g year:2017
|g number:23
|g day:05
|g month:09
|g pages:2007-2019
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| 856 |
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|u http://dx.doi.org/10.1002/jcc.24845
|3 Volltext
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