ReviewCurrent opinion in structural biology2017
Path-sampling strategies for simulating rare events in biomolecular systems.
Review in Current opinion in structural biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 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
52 citing papers in PubMed.
- Large-scale protein conformational transitions revealed by weighted ensemble simulations and EPR.Chemical science · 2026Article
- Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.Cell systems · 2026Article
- Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.bioRxiv : the preprint server for biology · 2026Article
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework.The journal of physical chemistry. A · 2026Article
- Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding.Journal of chemical theory and computation · 2025Article
- Targeted TPS Shooting Using Computer Vision to Generate Ensemble of Trajectories.Journal of chemical theory and computation · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias.Journal of chemical theory and computation · 2025Article
- Investigation into the effect of phenylalanine gating on anaerobic haem breakdown using the energy landscape approach.Protein science : a publication of the Protein Society · 2025Article
- Evaluation of Au(III) complexes as Plasmodium falciparum aquaglyceroporin (PfAQP) inhibitors by in silico and in vitro methods.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2024Article
- Gating residues govern ligand unbinding kinetics from the buried cavity in HIF-2α PAS-B.Protein science : a publication of the Protein Society · 2024Article
- Generating Protein Structures for Pathway Discovery Using Deep Learning.Journal of chemical theory and computation · 2024Article
- Rare-Event Sampling using a Reinforcement Learning-Based Weighted Ensemble Method.bioRxiv : the preprint server for biology · 2024Article
- Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.Journal of chemical theory and computation · 2024Article
- Structural biology in the age of X-ray free-electron lasers and exascale computing.Current opinion in structural biology · 2024Review
- Enhanced Sampling with Machine Learning.Annual review of physical chemistry · 2024Review
- Revisiting Textbook Azide-Clock Reactions: A "Propeller-Crawling" Mechanism Explains Differences in Rates.Journal of the American Chemical Society · 2024Article
- Fine-tuning activation specificity of G-protein-coupled receptors via automated path searching.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways.Journal of chemical information and modeling · 2023Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Despite more than three decades of effort with molecular dynamics simulations, long-timescale (ms and beyond) biologically relevant phenomena remain out of reach in most systems of interest. This is largely because important transitions, such as conformational changes and (un)binding events, tend to be rare for conventional simulations (<10μs). That is, conventional simulations will predominantly dwell in metastable states instead of making large transitions in complex biomolecular energy landscapes. In contrast, path sampling approaches focus computing effort specifically on transitions of interest. Such approaches have been in use for nearly 20 years in biomolecular systems and enabled the generation of pathways and calculation of rate constants for ms processes, including large protein conformational changes, protein folding, and protein (un)binding.
Indexed as
Identifiers
What OpenQuestion holds
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.