Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors
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Title
Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors
Authors
Keywords
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Journal
MOLECULES
Volume 22, Issue 2, Pages 340
Publisher
MDPI AG
Online
2017-02-23
DOI
10.3390/molecules22020340
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- (2016) Yi Shang et al. ACS Chemical Biology
- Identification of Two Distinct Sites for Antagonist and Biased Agonist Binding to the Human Chemokine Receptor CXCR3
- (2016) Lampros Milanos et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State That Selectively Triggers G Protein Signaling Pathways
- (2016) Sebastian Schneider et al. BIOCHEMISTRY
- Discovery of novel antagonists of human neurotensin receptor 1 on the basis of ligand and protein structure
- (2016) Guo Zhang et al. BIOMEDICINE & PHARMACOTHERAPY
- Biased agonism: An emerging paradigm in GPCR drug discovery
- (2016) Zoran Rankovic et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action
- (2016) Xianhai Yang et al. CHEMICAL RESEARCH IN TOXICOLOGY
- Structure-Based Virtual Screening for Dopamine D2Receptor Ligands as Potential Antipsychotics
- (2016) Agnieszka A. Kaczor et al. ChemMedChem
- Molecular interaction fingerprint approaches for GPCR drug discovery
- (2016) Márton Vass et al. CURRENT OPINION IN PHARMACOLOGY
- Evaluation of protein–ligand affinity prediction using steered molecular dynamics simulations
- (2016) Noriaki Okimoto et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- LEADS-PEP: A Benchmark Data Set for Assessment of Peptide Docking Performance
- (2016) Alexander Sebastian Hauser et al. Journal of Chemical Information and Modeling
- GPCR-Bench: A Benchmarking Set and Practitioners’ Guide for G Protein-Coupled Receptor Docking
- (2016) Dahlia R. Weiss et al. Journal of Chemical Information and Modeling
- Interplay between Two Allosteric Sites and Their Influence on Agonist Binding in Human μ Opioid Receptor
- (2016) Damian Bartuzi et al. Journal of Chemical Information and Modeling
- CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma
- (2016) Heather A. Carlson et al. Journal of Chemical Information and Modeling
- Yada: a novel tool for molecular docking calculations
- (2016) S. Piotto et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015
- (2016) Veronica Salmaso et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
- (2016) Symon Gathiaka et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand–Receptor Docking
- (2016) Robert B. Murphy et al. JOURNAL OF MEDICINAL CHEMISTRY
- The dopamine D2 receptor dimer and its interaction with homobivalent antagonists: homology modeling, docking and molecular dynamics
- (2016) Agnieszka A. Kaczor et al. JOURNAL OF MOLECULAR MODELING
- In silicoExploration of the Conformational Universe of GPCRs
- (2016) Ismael Rodríguez-Espigares et al. Molecular Informatics
- Incorporating QM and solvation into docking for applications to GPCR targets
- (2016) Minsup Kim et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor
- (2016) Yinglong Miao et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position
- (2016) Kevin W. Kastner et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction
- (2016) Chengfei Yan et al. STRUCTURE
- Cholesterol-dependent Conformational Plasticity in GPCR Dimers
- (2016) Xavier Prasanna et al. Scientific Reports
- Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4
- (2016) Kristyna Pluhackova et al. PLoS Computational Biology
- Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
- (2016) Samuel Hertig et al. PLoS Computational Biology
- Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description
- (2015) Francesca Spyrakis et al. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
- Covalent Docking Predicts Substrates for Haloalkanoate Dehalogenase Superfamily Phosphatases
- (2015) Nir London et al. BIOCHEMISTRY
- Novel Scaffold Identification of mGlu1 Receptor Negative Allosteric Modulators Using a Hierarchical Virtual Screening Approach
- (2015) Jae Wan Jang et al. Chemical Biology & Drug Design
- Fragment-Based Drug Discovery and Molecular Docking in Drug Design
- (2015) Tao Wang et al. CURRENT PHARMACEUTICAL BIOTECHNOLOGY
- Thematic Minireview Series: New Directions in G Protein-coupled Receptor Pharmacology
- (2015) Henrik G. Dohlman JOURNAL OF BIOLOGICAL CHEMISTRY
- Molecular modelling of human 5-hydroxytryptamine receptor (5-HT2A) and virtual screening studies towards the identification of agonist and antagonist molecules
- (2015) A. Gandhimathi et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- Activation and Allosteric Modulation of Human μ Opioid Receptor in Molecular Dynamics
- (2015) Damian Bartuzi et al. Journal of Chemical Information and Modeling
- A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics
- (2015) Quan Van Vuong et al. Journal of Chemical Information and Modeling
- Molecular Docking Screening Using Agonist-Bound GPCR Structures: Probing the A2A Adenosine Receptor
- (2015) David Rodríguez et al. Journal of Chemical Information and Modeling
- Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models
- (2015) Anirudh Ranganathan et al. JOURNAL OF MEDICINAL CHEMISTRY
- Minireview: Role of Intracellular Scaffolding Proteins in the Regulation of Endocrine G Protein-Coupled Receptor Signaling
- (2015) Cornelia Walther et al. MOLECULAR ENDOCRINOLOGY
- Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors
- (2015) Agnieszka A. Kaczor et al. Molecular Informatics
- NMR-Assisted Molecular Docking Methodologies
- (2015) Mattia Sturlese et al. Molecular Informatics
- Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65
- (2015) Xi-Ping Huang et al. NATURE
- GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
- (2015) Hasup Lee et al. NUCLEIC ACIDS RESEARCH
- Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
- (2015) Kalli Kappel et al. QUARTERLY REVIEWS OF BIOPHYSICS
- AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking
- (2015) Avraham Ben-Shimon et al. STRUCTURE
- Advances in Computational Techniques to Study GPCR–Ligand Recognition
- (2015) Antonella Ciancetta et al. TRENDS IN PHARMACOLOGICAL SCIENCES
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- (2014) Denis Schmidt et al. ACS Chemical Biology
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- (2014) David Rodríguez et al. STRUCTURE
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- (2013) Mu Gao et al. BIOINFORMATICS
- Recent Trends and Future Prospects in Computational GPCR Drug Discovery: From Virtual Screening to Polypharmacology
- (2013) Antonio Carrieri et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap
- (2013) Yue Yang et al. Expert Opinion on Drug Discovery
- Ligand-Optimized Homology Models of D1 and D2 Dopamine Receptors: Application for Virtual Screening
- (2013) Marcin Kołaczkowski et al. Journal of Chemical Information and Modeling
- The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs
- (2013) Ákos Tarcsay et al. Journal of Chemical Information and Modeling
- Complementarity between in Silico and Biophysical Screening Approaches in Fragment-Based Lead Discovery against the A2A Adenosine Receptor
- (2013) Dan Chen et al. Journal of Chemical Information and Modeling
- eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands
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- Modeling Complexes of Transmembrane Proteins: Systematic Analysis of ProteinProtein Docking Tools
- (2013) Agnieszka A. Kaczor et al. Molecular Informatics
- Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs
- (2013) Ron O. Dror et al. NATURE
- Activation and allosteric modulation of a muscarinic acetylcholine receptor
- (2013) Andrew C. Kruse et al. NATURE
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
- (2013) Kai J. Kohlhoff et al. Nature Chemistry
- Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
- (2013) Christopher D. Wassman et al. Nature Communications
- An analysis of oligomerization interfaces in transmembrane proteins
- (2013) Jose M Duarte et al. BMC STRUCTURAL BIOLOGY
- Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1
- (2012) Yaw Sing Tan et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Oligomerization of G Protein-Coupled Receptors: Computational Methods
- (2012) J. Selent et al. CURRENT MEDICINAL CHEMISTRY
- Oligomerization of G Protein-Coupled Receptors: Biochemical and Biophysical Methods
- (2012) A.A. Kaczor et al. CURRENT MEDICINAL CHEMISTRY
- Structure-Based Design in the GPCR Target Space
- (2012) M. Kontoyianni et al. CURRENT MEDICINAL CHEMISTRY
- Action of Molecular Switches in GPCRs - Theoretical and Experimental Studies
- (2012) B. Trzaskowski et al. CURRENT MEDICINAL CHEMISTRY
- Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints
- (2012) Francesco Sirci et al. Journal of Chemical Information and Modeling
- Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines
- (2012) Thijs Beuming et al. Journal of Chemical Information and Modeling
- Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
- (2012) Ahmet Bakan et al. Journal of Chemical Theory and Computation
- Water PMF for predicting the properties of water molecules in protein binding site
- (2012) Mingyue Zheng et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- A Prospective Cross-Screening Study on G-Protein-Coupled Receptors: Lessons Learned in Virtual Compound Library Design
- (2012) Marijn P. A. Sanders et al. JOURNAL OF MEDICINAL CHEMISTRY
- Optimization of Adenosine 5′-Carboxamide Derivatives as Adenosine Receptor Agonists Using Structure-Based Ligand Design and Fragment Screening
- (2012) Dilip K. Tosh et al. JOURNAL OF MEDICINAL CHEMISTRY
- Fractal dimension as a measure of surface roughness of G protein-coupled receptors: implications for structure and function
- (2012) Agnieszka A. Kaczor et al. JOURNAL OF MOLECULAR MODELING
- Crystal structure of the µ-opioid receptor bound to a morphinan antagonist
- (2012) Aashish Manglik et al. NATURE
- Structure and dynamics of the M3 muscarinic acetylcholine receptor
- (2012) Andrew C. Kruse et al. NATURE
- The Role of Water in Activation Mechanism of Human N-Formyl Peptide Receptor 1 (FPR1) Based on Molecular Dynamics Simulations
- (2012) Shuguang Yuan et al. PLoS One
- Structure-based drug screening for G-protein-coupled receptors
- (2012) Brian K. Shoichet et al. TRENDS IN PHARMACOLOGICAL SCIENCES
- New insights from structural biology into the druggability of G protein-coupled receptors
- (2012) Jonathan S. Mason et al. TRENDS IN PHARMACOLOGICAL SCIENCES
- Light on the structure of thromboxane A2 receptor heterodimers
- (2011) Francesca Fanelli et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors
- (2011) Jennifer M Johnston et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Structural aspects of M3 muscarinic acetylcholine receptor dimer formation and activation
- (2011) Jianxin Hu et al. FASEB JOURNAL
- Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H1Receptor
- (2011) Chris de Graaf et al. JOURNAL OF MEDICINAL CHEMISTRY
- How Does a Drug Molecule Find Its Target Binding Site?
- (2011) Yibing Shan et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Crystal structure of the β2 adrenergic receptor–Gs protein complex
- (2011) Søren G. F. Rasmussen et al. NATURE
- Ligand discovery from a dopamine D3 receptor homology model and crystal structure
- (2011) Jens Carlsson et al. Nature Chemical Biology
- Pathway and mechanism of drug binding to G-protein-coupled receptors
- (2011) Ron O. Dror et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
- (2011) I. Buch et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment
- (2011) Irina Kufareva et al. STRUCTURE
- Hetero-dimerization of serotonin 5-HT2A and dopamine D2 receptors
- (2010) Sylwia Łukasiewicz et al. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
- Mapping the Druggable Allosteric Space of G-Protein Coupled Receptors: a Fragment-Based Molecular Dynamics Approach
- (2010) Anthony Ivetac et al. Chemical Biology & Drug Design
- The Role of Water Molecules in Computational Drug Design
- (2010) Stephanie de Beer et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Accounting for water molecules in drug design
- (2010) Sergio E Wong et al. Expert Opinion on Drug Discovery
- Advances and Challenges in Protein-Ligand Docking
- (2010) Sheng-You Huang et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- A Lipid Pathway for Ligand Binding Is Necessary for a Cannabinoid G Protein-coupled Receptor
- (2010) Dow P. Hurst et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Evaluation of 1-arylpiperazine derivative of hydroxybenzamides as 5-HT1A and 5-HT7 serotonin receptor ligands: An experimental and molecular modeling approach
- (2010) Piotr Kowalski et al. JOURNAL OF HETEROCYCLIC CHEMISTRY
- Computational Mapping of the Conformational Transitions in Agonist Selective Pathways of a G-Protein Coupled Receptor
- (2010) Supriyo Bhattacharya et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor
- (2010) Christopher Higgs et al. ACS Medicinal Chemistry Letters
- Recent Advances in Structure-Based Virtual Screening of G-Protein Coupled Receptors
- (2009) Subramaniam Ananthan et al. AAPS Journal
- Structure-Based Design, Synthesis, and Biochemical and Pharmacological Characterization of Novel Salvinorin A Analogues as Active State Probes of the κ-Opioid Receptor
- (2009) Feng Yan et al. BIOCHEMISTRY
- Exploring Molecular Mechanisms of Ligand Recognition by Opioid Receptors with Metadynamics
- (2009) Davide Provasi et al. BIOCHEMISTRY
- Fpocket: An open source platform for ligand pocket detection
- (2009) Vincent Le Guilloux et al. BMC BIOINFORMATICS
- G protein-coupled receptor hetero-dimerization: contribution to pharmacology and function
- (2009) Graeme Milligan BRITISH JOURNAL OF PHARMACOLOGY
- G Protein-Coupled Receptors: Target-Based In Silico Screening
- (2009) Hanoch Senderowitz et al. CURRENT PHARMACEUTICAL DESIGN
- Molecular Dynamics Simulation of the Heterodimeric mGluR2/5HT2AComplex. An Atomistic Resolution Study of a Potential New Target in Psychiatric Conditions
- (2009) Agostino Bruno et al. Journal of Chemical Information and Modeling
- AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
- (2009) Oleg Trott et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- (2009) Garrett M. Morris et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Computational study of the heterodimerization between μ and δ receptors
- (2009) Xin Liu et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Prediction of the Water Content in Protein Binding Sites
- (2009) Julien Michel et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
- (2009) Mayako Michino et al. NATURE REVIEWS DRUG DISCOVERY
- Anton, a special-purpose machine for molecular dynamics simulation
- (2008) David E. Shaw et al. COMMUNICATIONS OF THE ACM
- Exploiting Ordered Waters in Molecular Docking
- (2008) Niu Huang et al. JOURNAL OF MEDICINAL CHEMISTRY
- Herkinorin Analogues with Differential β-Arrestin-2 Interactions
- (2008) Kevin Tidgewell et al. JOURNAL OF MEDICINAL CHEMISTRY
- Crystal structure of opsin in its G-protein-interacting conformation
- (2008) Patrick Scheerer et al. NATURE
- High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation
- (2008) C. Altenbach et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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