Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

We present a method to identify small molecule ligand binding sites and orientations to a given protein crystal structure using GPU-accelerated Hamiltonian replica exchange molecular dynamics simulations. The Hamiltonians used vary from the physical end state of protein interacting with the ligand t...

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Hauptverfasser: Wang, Kai, Yang, Yanzhi, Chodera, John D., Shirts, Michael R.
Format: Artigo
Sprache:Inglês
Veröffentlicht: 2013
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Article
Online Zugang:https://ncbi.nlm.nih.gov/pmc/articles/PMC4154199/
https://ncbi.nlm.nih.gov/pubmed/24297454
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1007/s10822-013-9689-8
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