ReviewQuarterly reviews of biophysics2011
Biomolecularmodeling and simulation: a field coming of age.
Review in Quarterly reviews of biophysics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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
45 citing papers in PubMed.
- Structural and Functional Impacts of SARS-CoV-2 Spike Protein Mutations: Insights From Predictive Modeling and Analytics.JMIR bioinformatics and biotechnology · 2025Article
- Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method.Journal of chemical theory and computation · 2025Article
- Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.Biophysical reviews · 2025Article
- Article
- Integrating computational methods andHeliyon · 2024Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces.The journal of physical chemistry letters · 2023Article
- Progress in Simulation Studies of Insulin Structure and Function.Frontiers in endocrinology · 2022Review
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- Biomolecular modeling thrives in the age of technology.Nature computational science · 2021Article
- A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature.The Journal of chemical physics · 2021Article
- Recent advances in design and applications of biomimetic self-assembled peptide hydrogels for hard tissue regeneration.Bio-design and manufacturing · 2021Review
- Solvation Free Energy of Self-Assembled Complexes: Using Molecular Dynamics to Understand the Separation of ssDNA-Wrapped Single-Walled Carbon Nanotubes.The journal of physical chemistry. C, Nanomaterials and interfaces · 2020Article
- Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability.The journal of physical chemistry letters · 2019Article
- Multiconfigurational Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2019Article
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Recent Trends and Applications of Molecular Modeling in GPCR⁻Ligand Recognition and Structure-Based Drug Design.International journal of molecular sciences · 2018Review
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
- FAST UPDATING MULTIPOLE COULOMBIC POTENTIAL CALCULATION.SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics · 2017Article
- Partially Assembled Nucleosome Structures at Atomic Detail.Biophysical journal · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field’s history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.
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.