Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors

Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors

(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CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma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

Identifying Modulators of CXC Receptors 3 and 4 with Tailored Selectivity Using Multi-Target Docking

(2014) Denis Schmidt et al.   ACS Chemical Biology

Virtual fragment screening on GPCRs: A case study on dopamine D3 and histamine H4 receptors

(2014) Márton Vass et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor

(2014) Eelke B. Lenselink et al.   Journal of Chemical Information and Modeling

Strategies for Improved Modeling of GPCR-Drug Complexes: Blind Predictions of Serotonin Receptors Bound to Ergotamine

(2014) David Rodríguez et al.   Journal of Chemical Information and Modeling

Steered Molecular Dynamics Simulations for Studying Protein–Ligand Interaction in Cyclin-Dependent Kinase 5

(2014) Jagdish Suresh Patel et al.   Journal of Chemical Information and Modeling

Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale

(2014) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

Structure-Based Virtual Screening of the Nociceptin Receptor: Hybrid Docking and Shape-Based Approaches for Improved Hit Identification

(2014) Pankaj R. Daga et al.   Journal of Chemical Information and Modeling

A Functional Selectivity Mechanism at the Serotonin-2A GPCR Involves Ligand-Dependent Conformations of Intracellular Loop 2

(2014) Jose Manuel Perez-Aguilar et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Application of BRET for Studying G Protein-Coupled Receptors

(2014) Agnieszka Kaczor et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

Structure-Based Discovery of Selective Serotonin 5-HT 1B Receptor Ligands

(2014) David Rodríguez et al.   STRUCTURE

Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges

(2014) Irina Kufareva et al.   STRUCTURE

Investigation of novel ropinirole analogues: synthesis, pharmacological evaluation and computational analysis of dopamine D2 receptor functionalized congeners and homobivalent ligands

(2014) Manuela Jörg et al.   MedChemComm

Conformation Guides Molecular Efficacy in Docking Screens of Activated β-2 Adrenergic G Protein Coupled Receptor

(2013) Dahlia R. Weiss et al.   ACS Chemical Biology

APoc: large-scale identification of similar protein pockets

(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

(2013) Michal Brylinski et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Modeling Complexes of Transmembrane Proteins: Systematic Analysis of ProteinProtein 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