ReviewComputational and structural biotechnology journal2020
Computational reconstruction of atomistic protein structures from coarse-grained models.
Review in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 58 citations in OpenAlex.
- AI-driven drug-target interaction prediction: current progress, challenges, and future roadmap for precision medicine.Journal of computer-aided molecular design · 2026Review
- Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.Biophysical journal · 2026Review
- Constraint Decoupled Latent Diffusion for Protein Backmapping.Journal of chemical theory and computation · 2026Article
- Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules.Journal of molecular biology · 2025Review
- Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations.Computational and structural biotechnology journal · 2024Article
- Exploring protein functions from structural flexibility using CABS-flex modeling.Protein science : a publication of the Protein Society · 2024Review
- Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers.Journal of chemical information and modeling · 2024Article
- ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures.Molecules (Basel, Switzerland) · 2024Article
- Structure prediction of linear and cyclic peptides using CABS-flex.Briefings in bioinformatics · 2024Article
- An end-to-end deep learning method for protein side-chain packing and inverse folding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022Review
- Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.PLoS computational biology · 2022Article
- Multiscale modelling of claudin-based assemblies: A magnifying glass for novel structures of biological interfaces.Computational and structural biotechnology journal · 2022Review
- Kinematic Reconstruction of Cyclic Peptides and Protein Backbones from Partial Data.Journal of chemical information and modeling · 2021Article
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.Journal of chemical information and modeling · 2021Article
- Computational Tools to Rationalize and Predict the Self-Assembly Behavior of Supramolecular Gels.Gels (Basel, Switzerland) · 2021Review
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Molecular Dynamics Scoring of Protein-Peptide Models Derived from Coarse-Grained Docking.Molecules (Basel, Switzerland) · 2021Article
- Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement.Briefings in bioinformatics · 2021Article
- DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Three-dimensional protein structures, whether determined experimentally or theoretically, are often too low resolution. In this mini-review, we outline the computational methods for protein structure reconstruction from incomplete coarse-grained to all atomistic models. Typical reconstruction schemes can be divided into four major steps. Usually, the first step is reconstruction of the protein backbone chain starting from the C-alpha trace. This is followed by side-chains rebuilding based on protein backbone geometry. Subsequently, hydrogen atoms can be reconstructed. Finally, the resulting all-atom models may require structure optimization. Many methods are available to perform each of these tasks. We discuss the available tools and their potential applications in integrative modeling pipelines that can transfer coarse-grained information from computational predictions, or experiment, to all atomistic structures.
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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.