ReviewInternational journal of molecular sciences2020
Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems.
Review in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 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
84 citing papers in PubMed, 1 synthesis or guideline pooled it, 183 citations in OpenAlex.
- 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
- 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
- The Shape of Things to Come: α-Helical Membrane Protein Folding on the Ribosome.Chemical reviews · 2026Review
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.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
- AutoPocket2CREST: Automating Binding Pocket Extraction for the CREST Conformer Generation Pipeline.Journal of chemical information and modeling · 2026Article
- AI-Driven Design of Miniproteins as Potential Allosteric Modulators.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Beyond MIDAS: AnACS omega · 2026Article
- Characterization of Conformational Instability of Monoclonal Antibodies During Chromatographic Purification.International journal of molecular sciences · 2026Review
- Computational design of constitutively active mutants of Dopamine D2 receptor inspired by ligand-independent activation mechanisms.BMC biology · 2026Article
- Exploring the GDP binding to KRasEuropean biophysics journal : EBJ · 2026Article
- Integrating Molecular Dynamics Simulations and Single-molecule FRET Spectroscopy: From Computational FRET Estimation to Experimental Data Interpretation.The journal of physical chemistry. B · 2026Review
- Ligand and structure-based toxicological assessment of (thio)semicarbazones on cholinesterases.Journal of computer-aided molecular design · 2026Article
- Molecular docking in histological biomarker discovery and disease modeling: techniques, validation, and translational perspectives.Journal of molecular histology · 2026Review
- Multiscale computational genomics in Wilson disease: from atomic dynamics to clinical prediction.Frontiers in genetics · 2026Review
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.bioRxiv : the preprint server for biology · 2025Article
- Targeting protein disorder: the next hurdle in drug discovery.Nature reviews. Drug discovery · 2025Review
- Computational Analysis ofACS chemical neuroscience · 2025Article
- Prediction of aggregation in monoclonal antibodies from molecular surface curvature.Scientific reports · 2025Article
- Frontier advances in molecular dynamics simulations for the design and optimization of oil-displacement polymers.RSC advances · 2025Review
24 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 at 1 institution in 1 country.
Funding
Abstract
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently could provide reliable answers to questions pertaining to the structure-function relationship of proteins. Data collated from protein dynamics can be translated into useful statistics that can be exploited to sieve thermodynamics and kinetics crucial for the elucidation of mechanisms responsible for the modulation of biological processes such as protein-ligand binding and protein-protein association. Continuous modernization of simulation tools enables accurate prediction and characterization of the aforementioned mechanisms and these qualities are highly beneficial for the expedition of drug development when effectively applied to structure-based drug design (SBDD). In this review, current all-atom MD simulation methods, with focus on enhanced sampling techniques, utilized to examine protein structure, dynamics, and functions are discussed. This review will pivot around computer calculations of protein-ligand and protein-protein systems with applications to SBDD. In addition, we will also be highlighting limitations faced by current simulation tools as well as the improvements that have been made to ameliorate their efficiency.
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.