Literature DB >> 35776320

Fully Flexible Ligand Docking for the P2X7 Receptor Using ROSIE.

Sudad Dayl1, Ralf Schmid2,3.   

Abstract

The availability of P2X7 receptor structures with allosteric antagonists bound enables us to predict specific interactions between receptor and antagonists at atomistic detail. In this chapter we outline how modern ligand docking techniques can be employed by the nonexpert to predict putative binding modes for known or hypothetical allosteric P2X7 antagonists.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Ligand docking; P2X receptor; P2X7R; ROSIE; Rosetta ligand

Mesh：

Substances：

Year:  2022        PMID： 35776320     DOI： 10.1007/978-1-0716-2384-8_4

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  14 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Discovery and Structure Relationships of Salicylanilide Derivatives as Potent, Non-acidic P2X1 Receptor Antagonists.

Authors:  Maoqun Tian; Aliaa Abdelrahman; Younis Baqi; Eduardo Fuentes; Djamil Azazna; Claudia Spanier; Sabrina Densborn; Sonja Hinz; Ralf Schmid; Christa E Müller
Journal:  J Med Chem       Date:  2020-05-27       Impact factor: 7.446

3.  Small-molecule ligand docking into comparative models with Rosetta.

Authors:  Steven A Combs; Samuel L Deluca; Stephanie H Deluca; Gordon H Lemmon; David P Nannemann; Elizabeth D Nguyen; Jordan R Willis; Jonathan H Sheehan; Jens Meiler
Journal:  Nat Protoc       Date:  2013-06-06       Impact factor: 13.491

4.  Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand.

Authors:  Samuel DeLuca; Karen Khar; Jens Meiler
Journal:  PLoS One       Date:  2015-07-24       Impact factor: 3.240

5.  ZINC 15--Ligand Discovery for Everyone.

Authors:  Teague Sterling; John J Irwin
Journal:  J Chem Inf Model       Date:  2015-11-09       Impact factor: 4.956

6.  Structural basis for subtype-specific inhibition of the P2X7 receptor.

Authors:  Akira Karasawa; Toshimitsu Kawate
Journal:  Elife       Date:  2016-12-09       Impact factor: 8.140

7.  Unique residues in the ATP gated human P2X7 receptor define a novel allosteric binding pocket for the selective antagonist AZ10606120.

Authors:  Rebecca C Allsopp; Sudad Dayl; Ralf Schmid; Richard J Evans
Journal:  Sci Rep       Date:  2017-04-07       Impact factor: 4.379

8.  Mapping the Allosteric Action of Antagonists A740003 and A438079 Reveals a Role for the Left Flipper in Ligand Sensitivity at P2X7 Receptors.

Authors:  Rebecca C Allsopp; Sudad Dayl; Anfal Bin Dayel; Ralf Schmid; Richard J Evans
Journal:  Mol Pharmacol       Date:  2018-03-13       Impact factor: 4.436

9.  An Allosteric Inhibitory Site Conserved in the Ectodomain of P2X Receptor Channels.

Authors:  Ariel R Ase; Éric Therrien; Philippe Séguéla
Journal:  Front Cell Neurosci       Date:  2019-04-09       Impact factor: 5.505

10.  Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).

Authors:  Sergey Lyskov; Fang-Chieh Chou; Shane Ó Conchúir; Bryan S Der; Kevin Drew; Daisuke Kuroda; Jianqing Xu; Brian D Weitzner; P Douglas Renfrew; Parin Sripakdeevong; Benjamin Borgo; James J Havranek; Brian Kuhlman; Tanja Kortemme; Richard Bonneau; Jeffrey J Gray; Rhiju Das
Journal:  PLoS One       Date:  2013-05-22       Impact factor: 3.240
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