ReviewCurrent opinion in structural biology2016
Advances in free-energy-based simulations of protein folding and ligand binding.
Review in Current opinion in structural biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 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
60 citing papers in PubMed.
- Determinants of Protein Folding Pathways: Lessons from Metamorphic Proteins.International journal of molecular sciences · 2026Review
- Structural mechanisms underlying distinct binding and activities of 18:0 and 18:1 lysophosphatidic acids at LPA1 receptor.PLoS computational biology · 2026Article
- The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.ACS omega · 2026Article
- Cholinergic Inhibition and Antioxidant Potential of Gongronema latifolium Benth Leaf in Neurodegeneration: Experimental and In Silico Study.Cell biochemistry and biophysics · 2025Article
- Apoptotic Potential of Iloneoside from Gongronema latifolium Benth against Prostate Cancer Cells Using In Vitro and In Silico Approach.Cell biochemistry and biophysics · 2025Article
- Accurate protein-ligand binding free energy estimation using QM/MM on multi-conformers predicted from classical mining minima.Communications chemistry · 2024Article
- Identification of potential inhibitors of cholinergic and β-secretase enzymes from phytochemicals derived from Gongronema latifolium Benth leaf: an integrated computational analysis.Molecular diversity · 2024Article
- Applications of Molecular Dynamics Simulations in Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Antispasmodic Effect ofMolecules (Basel, Switzerland) · 2023Article
- Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.Journal of chemical theory and computation · 2023Article
- Atomistic simulations suggest dietary flavonoids from Beta vulgaris (beet) as promising inhibitors of human angiotensin-converting enzyme and 2-alpha-adrenergic receptors in hypertension.Bioinformatics advances · 2023Article
- Pre-Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- African derived phytocompounds may interfere with SARS-CoV-2 RNA capping machinery via inhibition of 2'-O-ribose methyltransferase: AnJournal of molecular structure · 2022Article
- The binding and specificity of chemokine binding proteins, through the lens of experiment and computation.Biomedical journal · 2022Review
- Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers.Journal of chemical theory and computation · 2022Article
- Molecular Docking Simulation Studies Identifies Potential Natural Product Derived-Antiwolbachial Compounds as Filaricides against Onchocerciasis.Biomedicines · 2021Article
- Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field.Journal of chemical theory and computation · 2021Article
- Dietary stigmastane-type saponins as promising dual-target directed inhibitors of SARS-CoV-2 proteases: a structure-based screening.RSC advances · 2021Article
- SARS-CoV-2 host cell entry: an in silico investigation of potential inhibitory roles of terpenoids.Journal, genetic engineering & biotechnology · 2021Article
- Dual targeting of cytokine storm and viral replication in COVID-19 by plant-derived steroidal pregnanes: An in silico perspective.Computers in biology and medicine · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Free-energy-based simulations are increasingly providing the narratives about the structures, dynamics and biological mechanisms that constitute the fabric of protein science. Here, we review two recent successes. It is becoming practical: first, to fold small proteins with free-energy methods without knowing substructures and second, to compute ligand-protein binding affinities, not just their binding poses. Over the past 40 years, the timescales that can be simulated by atomistic MD are doubling every 1.3 years--which is faster than Moore's law. Thus, these advances are not simply due to the availability of faster computers. Force fields, solvation models and simulation methodology have kept pace with computing advancements, and are now quite good. At the tip of the spear recently are GPU-based computing, improved fast-solvation methods, continued advances in force fields, and conformational sampling methods that harness external information.
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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.