ArticleAnnual reports in computational chemistry2009
Methods for Monte Carlo simulations of biomacromolecules.
Article in Annual reports in computational chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
- Chain collapse, reduced dielectric, and water release drive protein phase separation.Biophysical journal · 2026Article
- RNA polymerase II CTD Ser5 phosphorylation induces competing effects of expansion and compaction.Biophysical journal · 2026Article
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- pH Sensitivity of the SERF1a Conformational Ensemble.ACS omega · 2026Article
- Direct Optical Quantification of Chain Collapse, Reduced Dielectric, and Water Release Driving Protein Phase Separation.bioRxiv : the preprint server for biology · 2025Article
- Matrin-3 forms spherical and wormlike assemblies that are modulated by RNA binding and ALS/FTD-associated mutations.Molecular cell · 2025Article
- Disrupting Amyloid Filaments of Tau by Means of Electric Fields.The journal of physical chemistry. B · 2025Article
- Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates.Cell · 2025Article
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- Optimizing number of Raman spectra using an artificial neural network guided Monte Carlo simulation approach to analyze human cortical bone.Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy · 2025Article
- Review
- Molecular insights into the interaction between a disordered protein and a folded RNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Phosphorylation of disordered proteins tunes local and global intramolecular interactions.Biophysical journal · 2024Article
- Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins.PNAS nexus · 2024Article
- High-throughput affinity measurements of direct interactions between activation domains and co-activators.bioRxiv : the preprint server for biology · 2024Article
- Expanding the molecular language of protein liquid-liquid phase separation.Nature chemistry · 2024Article
- Molecular insights into the interaction between a disordered protein and a folded RNA.bioRxiv : the preprint server for biology · 2024Article
- Phosphorylation of disordered proteins tunes local and global intramolecular interactions.bioRxiv : the preprint server for biology · 2024Article
- Transferable deep generative modeling of intrinsically disordered protein conformations.PLoS computational biology · 2024Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
The state-of-the-art for Monte Carlo (MC) simulations of biomacromolecules is reviewed. Available methodologies for sampling conformational equilibria and associations of biomacromolecules in the canonical ensemble, given a continuum description of the solvent environment, are reviewed. Detailed sections are provided dealing with the choice of degrees of freedom, the efficiencies of MC algorithms and algorithmic peculiarities, as well as the optimization of simple movesets. The issue of introducing correlations into elementary MC moves, and the applicability of such methods to simulations of biomacromolecules is discussed. A brief discussion of multicanonical methods and an overview of recent simulation work highlighting the potential of MC methods are also provided. It is argued that MC simulations, while underutilized biomacromolecular simulation community, hold promise for simulations of complex systems and phenomena that span multiple length scales, especially when used in conjunction with implicit solvation models or other coarse graining strategies.
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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.