ArticleWiley interdisciplinary reviews. Computational molecular science
Computational protein structure refinement: Almost there, yet still so far to go.
Article in Wiley interdisciplinary reviews. Computational molecular science. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
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- High-speed atomic force microscopy and 3D modeling reveal the structural dynamics of ADAR1 complexes.Nature communications · 2025Article
- Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules.Journal of molecular biology · 2025Review
- Investigation into in silico and in vitro approaches for inhibitors targeting MCM10 in Leishmania donovani: a comprehensive study.Molecular diversity · 2025Article
- In silico design and assessment of a multi-epitope peptide vaccine against multidrug-resistantIn silico pharmacology · 2025Article
- Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds.Scientific reports · 2023Article
- Chemical Features and Machine Learning Assisted Predictions of Protein-Ligand Short Hydrogen Bonds.Research square · 2023Article
- Vaccinomics-Aided Development of a Next-Generation Chimeric Vaccine against an Emerging Threat:Vaccines · 2022Article
- Effective prediction of short hydrogen bonds in proteins via machine learning method.Scientific reports · 2022Article
- Modelling of C-terminal tail of human STING and its interaction with tank-binding kinase 1.Turkish journal of biology = Turk biyoloji dergisi · 2022Article
- Comparative molecular docking and molecular-dynamic simulation of wild-type- and mutant carboxylesterase with BTA-hydrolase for enhanced binding to plastic.Engineering in life sciences · 2022Article
- Article
- Improved 3-D Protein Structure Predictions using Deep ResNet Model.The protein journal · 2021Article
- Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement.Nature communications · 2021Article
- "Dividing and Conquering" and "Caching" in Molecular Modeling.International journal of molecular sciences · 2021Review
- Molecular free energy optimization on a computational graph.RSC advances · 2021Article
- Targeting Bromodomain and Extraterminal Proteins for Drug Discovery: From Current Progress to Technological Development.Journal of medicinal chemistry · 2021Review
- Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
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Abstract
Protein structures are essential in modern biology yet experimental methods are far from being able to catch up with the rapid increase in available genomic data. Computational protein structure prediction methods aim to fill the gap while the role of protein structure refinement is to take approximate initial template-based models and bring them closer to the true native structure. Current methods for computational structure refinement rely on molecular dynamics simulations, related sampling methods, or iterative structure optimization protocols. The best methods are able to achieve moderate degrees of refinement but consistent refinement that can reach near-experimental accuracy remains elusive. Key issues revolve around the accuracy of the energy function, the inability to reliably rank multiple models, and the use of restraints that keep sampling close to the native state but also limit the degree of possible refinement. A different aspect is the question of what exactly the target of high-resolution refinement should be as experimental structures are affected by experimental conditions and different biological questions require varying levels of accuracy. While improvement of the global protein structure is a difficult problem, high-resolution refinement methods that improves local structural quality such as favorable stereochemistry and the avoidance of atomic clashes are much more successful.
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