Journal Article FZJ-2020-02855

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Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-based Hybrid Molecular Mechanics/Coarse-Grained Approach

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2020
American Chemical Society64160 Washington, DC

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Abstract: Human G protein-coupled receptors (hGPCRs) are the most frequent targets of Food and Drug Administration (FDA)-approved drugs. Structural bioinformatics, along with molecular simulation, can support structure-based drug design targeting hGPCRs. In this context, several years ago, we developed a hybrid molecular mechanics (MM)/coarse-grained (CG) approach to predict ligand poses in low-resolution hGPCR models. The approach was based on the GROMOS96 43A1 and PRODRG united-atom force fields for the MM part. Here, we present a new MM/CG implementation using, instead, the Amber 14SB and GAFF all-atom potentials for proteins and ligands, respectively. The new implementation outperforms the previous one, as shown by a variety of applications on models of hGPCR/ligand complexes at different resolutions, and it is also more user-friendly. Thus, it emerges as a useful tool to predict poses in low-resolution models and provides insights into ligand binding similarly to all-atom molecular dynamics, albeit at a lower computational cost.

Classification:

Contributing Institute(s):
  1. Computational Biomedicine (INM-9)
  2. Computational Biomedicine (IAS-5)
  3. Jara-Institut Quantum Information (INM-11)
Research Program(s):
  1. 574 - Theory, modelling and simulation (POF3-574) (POF3-574)

Appears in the scientific report 2020
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Medline ; Embargoed OpenAccess ; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; Essential Science Indicators ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; NationallizenzNationallizenz ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Web of Science Core Collection
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 Record created 2020-08-14, last modified 2021-02-08


Published on 2020-07-31. Available in OpenAccess from 2021-07-31.:
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