ReviewCurrent opinion in structural biology2011
Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors.
Review in Current opinion in structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
42 citing papers in PubMed.
- Unveiling Conformational States of CDK6 Caused by Binding of Vcyclin Protein and Inhibitor by Combining Gaussian Accelerated Molecular Dynamics and Deep Learning.Molecules (Basel, Switzerland) · 2024Article
- Article
- Predicting Biomolecular Binding Kinetics: A Review.Journal of chemical theory and computation · 2023Review
- Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors.Research square · 2023Article
- Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors.bioRxiv : the preprint server for biology · 2023Article
- Gaussian Accelerated Molecular Dynamics in OpenMM.The journal of physical chemistry. B · 2022Article
- Molecular Simulations and Drug Discovery of Adenosine Receptors.Molecules (Basel, Switzerland) · 2022Review
- GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling.Journal of chemical theory and computation · 2022Article
- Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs.Advances in protein chemistry and structural biology · 2022Review
- Challenges and frontiers of computational modelling of biomolecular recognition.QRB discovery · 2022Article
- Mechanism of Peptide Agonist Binding in CXCR4 Chemokine Receptor.Frontiers in molecular biosciences · 2022Article
- Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives.Advances and applications in bioinformatics and chemistry : AABC · 2022Review
- Computational Simulation of Holin S105 in Membrane Bilayer and Its Dimerization Through a Helix-Turn-Helix Motif.The Journal of membrane biology · 2021Article
- Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study.Biomolecules · 2021Article
- Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping.Journal of chemical theory and computation · 2019Article
- Recent advances in computational studies of GPCR-G protein interactions.Advances in protein chemistry and structural biology · 2019Review
- Interaction of POPC, DPPC, and POPE with the μ opioid receptor: A coarse-grained molecular dynamics study.PloS one · 2019Article
- A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue.Scientific reports · 2018Article
- Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.Journal of chemical theory and computation · 2018Article
- Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Despite many years of dedicated efforts, high-resolution structural determination of membrane proteins lags far behind that of soluble proteins. Computational methods in general, and molecular dynamics (MD) simulations in particular, have represented important alternative resources over the years to advance understanding of membrane protein structure and function. However, it is only recently that much progress has been achieved owing to new high-resolution membrane protein structures, specialized parallel computer architectures, and efficient simulation algorithms. This has definitely been the case for G protein-coupled receptors (GPCRs), which have assumed a leading role in the area of structural biology with several new structures appearing in the literature during the past five years. We provide here a concise overview of recent developments in computational biophysics of membrane proteins, using GPCRs as an example to showcase important information that can be derived from modern MD simulations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.