ArticleScientific reports2020
Sampling of the conformational landscape of small proteins with Monte Carlo methods.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era.Briefings in bioinformatics · 2025Review
- Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules.Journal of molecular biology · 2025Review
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
- dyphAI dynamic pharmacophore modeling with AI: a tool for efficient screening of new acetylcholinesterase inhibitors.Frontiers in chemistry · 2025Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 2024Article
- The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study.Physical chemistry chemical physics : PCCP · 2024Article
- Computational biology and artificial intelligence in mRNA vaccine design for cancer immunotherapy.Frontiers in cellular and infection microbiology · 2024Review
- Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins.Molecular cell · 2023Article
- Article
- Modeling Protein Complexes and Molecular Assemblies Using Computational Methods.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles.International journal of molecular sciences · 2022Article
- Modeling of protein conformational changes with Rosetta guided by limited experimental data.Structure (London, England : 1993) · 2022Article
- AlphaFold 2 and NMR Spectroscopy: Partners to Understand Protein Structure, Dynamics and Function.Frontiers in molecular biosciences · 2022Review
- A Minireview on Temperature Dependent Protein Conformational Sampling.The protein journal · 2021Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations. For this reason, many biologically interesting questions cannot be addressed using accessible state-of-the-art computational resources. Here, we report the development of an all-atom Monte Carlo approach that permits the modelling of the large-scale conformational change of proteins using standard off-the-shelf computational hardware and standard all-atom force fields. We demonstrate extensive thermodynamic characterization of the folding process of the α-helical Trp-cage, the Villin headpiece and the β-sheet WW-domain. We fully characterize the free energy landscape, transition states, energy barriers between different states, and the per-residue stability of individual amino acids over a wide temperature range. We demonstrate that a state-of-the-art intramolecular force field can be combined with an implicit solvent model to obtain a high quality of the folded structures and also discuss limitations that still remain.
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