Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach

scientific article

Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1111/J.1747-0285.2010.01012.X
P932PMC publication ID2918726
P698PubMed publication ID20626410
P5875ResearchGate publication ID45183651

P50authorJ. Andrew McCammonQ6104601
P2093author name stringAnthony Ivetac
P2860cites workPredicting slow structural transitions in macromolecular systems: Conformational floodingQ21686247
Canonical dynamics: Equilibrium phase-space distributionsQ21709091
Functional Selectivity and Classical Concepts of Quantitative PharmacologyQ22242288
MUSCLE: multiple sequence alignment with high accuracy and high throughputQ24613456
The impact of GPCR structures on pharmacology and structure-based drug designQ24628661
Critical Role for the Second Extracellular Loop in the Binding of Both Orthosteric and Allosteric G Protein-coupled Receptor LigandsQ57838214
Sustained activation of a G protein-coupled receptor via "anchored" agonist binding. Molecular localization of the salmeterol exosite within the 2-adrenergic receptorQ71514922
Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observationsQ24645752
Flexible ligand docking to multiple receptor conformations: a practical alternativeQ24650066
The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonistQ24654563
High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptorQ24657484
The selectivity of beta-adrenoceptor antagonists at the human beta1, beta2 and beta3 adrenoceptorsQ24670735
Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptorQ27646733
Crystal structure of the human beta2 adrenergic G-protein-coupled receptorQ27648868
A Specific Cholesterol Binding Site Is Established by the 2.8 Å Structure of the Human β2-Adrenergic ReceptorQ27650801
Structure of a beta1-adrenergic G-protein-coupled receptorQ27651011
Crystal structure of opsin in its G-protein-interacting conformationQ27652301
VMD: visual molecular dynamicsQ27860554
Comparative protein modelling by satisfaction of spatial restraintsQ27860866
GROMACS: fast, flexible, and freeQ27860998
GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor functionQ28254935
How many drug targets are there?Q28276660
The MARTINI force field: coarse grained model for biomolecular simulationsQ29617215
PocketPicker: analysis of ligand binding-sites with shape descriptors.Q30364721
Fast procedure for reconstruction of full-atom protein models from reduced representations.Q30367164
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.Q30367220
Coarse-grained MD simulations of membrane protein-bilayer self-assembly.Q30368740
A computational procedure for determining energetically favorable binding sites on biologically important macromoleculesQ30406755
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniquesQ33403707
Structure-based discovery of beta2-adrenergic receptor ligandsQ33426241
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidaseQ33466833
Accommodating protein flexibility in computational drug designQ33825095
Locating and characterizing binding sites on proteinsQ34066761
Allosteric binding sites on cell-surface receptors: novel targets for drug discoveryQ34139176
Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitorsQ34175711
GCRDb: a G-protein-coupled receptor databaseQ34333530
Seven-transmembrane-spanning receptors and heart functionQ34503394
G protein-coupled receptor allosterism and complexingQ34523552
Discovery of a novel binding trench in HIV integrase.Q34546744
Allosteric enhancers, allosteric agonists and ago-allosteric modulators: where do they bind and how do they act?Q34581080
G-protein-coupled receptors and cancer.Q34606002
Efficacy at G-protein-coupled receptorsQ34742798
Discovery of new GPCR biology: one receptor structure at a timeQ34920862
Implications of protein flexibility for drug discoveryQ35167908
Allosteric modulators of G-protein-coupled receptorsQ35559684
Fragment-based lead discoveryQ35852295
Allosteric modulation of G protein-coupled receptors: perspectives and recent developmentsQ35902519
Searching for new allosteric sites in enzymesQ35975051
G-protein signaling: back to the futureQ36061579
Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambinQ36280885
Molecular dynamics: survey of methods for simulating the activity of proteinsQ36472758
Ligand-stabilized conformational states of human beta(2) adrenergic receptor: insight into G-protein-coupled receptor activationQ36481447
An improved relaxed complex scheme for receptor flexibility in computer-aided drug designQ36838120
Conformational complexity of G-protein-coupled receptorsQ36880905
Novel selective allosteric activator of the M1 muscarinic acetylcholine receptor regulates amyloid processing and produces antipsychotic-like activity in rats.Q36959071
Allosteric modulation of kinases and GPCRs: design principles and structural diversityQ37110414
Structural insights into G-protein-coupled receptor activationQ37310590
The function of G-protein coupled receptors and membrane cholesterol: specific or general interaction?Q37340347
Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disordersQ37360436
Allosteric modulators of g protein-coupled receptors: future therapeutics for complex physiological disorders.Q37416470
Orthosteric/allosteric bitopic ligands: going hybrid at GPCRs.Q37547722
Ligands, their receptors and ... plasma membranesQ37568526
Rational design of dualsteric GPCR ligands: quests and promiseQ37688232
Stabilization of the human beta2-adrenergic receptor TM4-TM3-TM5 helix interface by mutagenesis of Glu122(3.41), a critical residue in GPCR structureQ40020328
The family of G‐protein‐coupled receptorsQ40439041
Identification of an allosteric binding site for Zn2+ on the beta2 adrenergic receptorQ40693273
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperatureQ41775672
Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.Q42943551
Computational drug design accommodating receptor flexibility: the relaxed complex schemeQ43992973
Computational approaches to identifying and characterizing protein binding sites for ligand designQ45327964
Accelerated molecular dynamics: a promising and efficient simulation method for biomoleculesQ46058456
Coupling ligand structure to specific conformational switches in the beta2-adrenoceptorQ46120520
From agonist to antagonist: Fab fragments of an agonist-like monoclonal anti-beta(2)-adrenoceptor antibody behave as antagonistsQ46208108
Use of the X-ray structure of the beta2-adrenergic receptor for drug discovery. Part 2: Identification of active compoundsQ46336635
Atypical muscarinic allosteric modulation: cooperativity between modulators and their atypical binding topology in muscarinic M2 and M2/M5 chimeric receptorsQ46699162
Crystallizing thinking about the beta2-adrenergic receptor.Q46779816
G protein-coupled receptors. I. Diversity of receptor-ligand interactionsQ47892279
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.Q48498889
Identification of hot spots within druggable binding regions by computational solvent mapping of proteins.Q51922140
Allosteric Modulation of G Protein–Coupled ReceptorsQ56115675
Insights into signaling from the β2-adrenergic receptor structureQ56648606
GROMACS 3.0: a package for molecular simulation and trajectory analysisQ57082068
P433issue3
P921main subjectG protein-coupled receptorQ38173
P304page(s)201-217
P577publication date2010-07-05
P1433published inChemical Biology and Drug DesignQ15749458
P1476titleMapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach
P478volume76

Reverse relations

cites work (P2860)
Q90568175Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities
Q36263056Allosteric "beta-blocker" isolated from a DNA-encoded small molecule library
Q31148716An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis
Q64110733Analysis of tractable allosteric sites in G protein-coupled receptors
Q36009999Bioinformatics and variability in drug response: a protein structural perspective
Q37582165Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
Q30521288Comparison of dynamics of extracellular accesses to the β(1) and β(2) adrenoceptors binding sites uncovers the potential of kinetic basis of antagonist selectivity
Q35967903Computational Advances for the Development of Allosteric Modulators and Bitopic Ligands in G Protein-Coupled Receptors
Q27311564Computational study on the different ligands induced conformation change of β2 adrenergic receptor-Gs protein complex
Q36072549Conformationally selective RNA aptamers allosterically modulate the β2-adrenoceptor.
Q33922348Differences in allosteric communication pipelines in the inactive and active states of a GPCR.
Q38795153Discovery of Novel Allosteric Eg5 Inhibitors Through Structure-Based Virtual Screening
Q35926542Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology
Q24633124Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
Q38109928Druggable orthosteric and allosteric hot spots to target protein-protein interactions.
Q30358225Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.
Q27308091Endogenous vs Exogenous Allosteric Modulators in GPCRs: A dispute for shuttling CB1 among different membrane microenvironments
Q28534702Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin
Q30391745Exploration of the conformational landscape in pregnane X receptor reveals a new binding pocket
Q27001129Exploring the role of receptor flexibility in structure-based drug discovery
Q42209394Force distribution reveals signal transduction in E. coli Hsp90.
Q35234897Identification of a novel selective serotonin reuptake inhibitor by coupling monoamine transporter-based virtual screening and rational molecular hybridization
Q41015632Identification of small-molecule binding pockets in the soluble monomeric form of the Aβ42 peptide
Q42183818Identification of the binding site of an allosteric ligand using STD-NMR, docking, and CORCEMA-ST calculations
Q35977592Intracellular Loop 2 Peptides of the Human 5HT1a Receptor are Differential Activators of Gi.
Q33577530Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor
Q46049863Mapping the allosteric sites of the A2A adenosine receptor.
Q93087286Mechanism of β2AR regulation by an intracellular positive allosteric modulator
Q34061019Molecular dynamics simulations and drug discovery
Q30369875Molecular dynamics simulations: from structure function relationships to drug discovery.
Q42582195Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site
Q35733861Molecular recognition in the case of flexible targets
Q36682460Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction
Q47348671Opportunities and Challenges in the Discovery of Allosteric Modulators of GPCRs
Q90430431Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations
Q35073109Predictive power of molecular dynamics receptor structures in virtual screening
Q38362491Principles in the design of ligand-targeted cancer therapeutics and imaging agents.
Q39152860Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors
Q26747130Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
Q38675922Signaling within Allosteric Machines: Signal Transmission Pathways Inside G Protein-Coupled Receptors.
Q35882569Structure-based model of allostery predicts coupling between distant sites
Q36604792The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

Search more.