ReviewBiochimica et biophysica acta2015
Enhanced sampling techniques in molecular dynamics simulations of biological systems.
Review in Biochimica et biophysica acta, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 265 papers, 1 of them a synthesis that pooled it.
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
265 citing papers in PubMed, 1 synthesis or guideline pooled it.
- In Silico Screening of Therapeutic Targets as a Tool to Optimize the Development of Drugs and Nutraceuticals in the Treatment of DiabetesInternational journal of molecular sciences · 2024Pooled it
- Article
- From Enhanced Sampling to Human-Readable Representations of Protein Dynamics.Journal of chemical theory and computation · 2026Article
- Conformational landscape of 2-aminopurine-substituted RNA oligonucleotides from machine-learning-driven enhanced sampling.Physical chemistry chemical physics : PCCP · 2026Article
- A Bayesian Approach to Interpret Time-Resolved Experiments Using Molecular Simulations.ACS physical chemistry Au · 2026Article
- Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling.Journal of chemical theory and computation · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Elucidating the Structure and Activation Mechanisms of GPCRs Using Modern Computational and AI Tools.Cell biochemistry and biophysics · 2026Review
- Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking.Journal of chemical theory and computation · 2026Article
- An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.Journal of chemical information and modeling · 2026Article
- Structuring Disorder via Supervised Molecular Dynamics: Uncovering Arginine-Glycine-Glycine-Mediated Ribonucleic Acid-Intrinsically Disordered Region Recognition Mechanisms.Journal of chemical information and modeling · 2026Article
- Quantum computing applications in drug discovery.Briefings in bioinformatics · 2026Review
- The evolving landscape of molecular visualization.Protein science : a publication of the Protein Society · 2026Review
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- Ensemble Sensitivity to Chemical Modifications in Free and Bound Macrocyclic Peptides.The journal of physical chemistry. B · 2026Article
- Uncertainty Quantification forChemical reviews · 2026Review
- eSIG-Net: Accurate prediction of single-mutation induced perturbations on protein interactions using a language model.bioRxiv : the preprint server for biology · 2026Article
- A Computational Framework to Evaluate Interactions of BPA and Its Analogs with Human Liver X Receptor-Beta for Health Risk Assessment.Chemical research in toxicology · 2026Article
- Protein structural dynamics in covalent drug design: insights from irreversible and reversible covalent inhibitors.RSC chemical biology · 2026Review
- Deconvolution of High-Dimensional Ion Mobility Data Using Reversible-Jump Markov Chain Monte Carlo.Analytical chemistry · 2026Article
205 more citing papers are in PubMed but not listed here.
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
backgroundMolecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. SCOPE OF REVIEW: In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. MAJOR
conclusionsEnhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. GENERAL SIGNIFICANCE: Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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.