ReviewCritical reviews in biochemistry and molecular biology2018
Finding the needle in the haystack: towards solving the protein-folding problem computationally.
Review in Critical reviews in biochemistry and molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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.
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Who cites it
13 citing papers in PubMed.
- Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins.Protein science : a publication of the Protein Society · 2025Article
- Biology and medicine in the landscape of quantum advantages.Journal of the Royal Society, Interface · 2022Review
- Protein folding in vitro and in the cell: From a solitary journey to a team effort.Biophysical chemistry · 2022Review
- Refolding of Lysozyme in Glycerol as Studied by Fast Scanning Calorimetry.International journal of molecular sciences · 2022Article
- Improved Protein Structure Prediction Using a New Multi-Scale Network and Homologous Templates.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Substrate Channeling by a Rationally Designed Fusion Protein in a Biocatalytic Cascade.JACS Au · 2021Article
- A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins.Journal of proteome research · 2021Article
- Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- Deep Learning in Protein Structural Modeling and Design.Patterns (New York, N.Y.) · 2020Review
- Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.PLoS computational biology · 2020Article
- Interfaces Between Alpha-helical Integral Membrane Proteins: Characterization, Prediction, and Docking.Computational and structural biotechnology journal · 2019Article
- Comparison of Peptide Ion Conformers Arising from Non-Helical and Helical Peptides Using Ion Mobility Spectrometry and Gas-Phase Hydrogen/Deuterium Exchange.Journal of the American Society for Mass Spectrometry · 2018Article
- Combined approaches from physics, statistics, and computer science forF1000Research · 2018Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Prediction of protein tertiary structures from amino acid sequence and understanding the mechanisms of how proteins fold, collectively known as "the protein folding problem," has been a grand challenge in molecular biology for over half a century. Theories have been developed that provide us with an unprecedented understanding of protein folding mechanisms. However, computational simulation of protein folding is still difficult, and prediction of protein tertiary structure from amino acid sequence is an unsolved problem. Progress toward a satisfying solution has been slow due to challenges in sampling the vast conformational space and deriving sufficiently accurate energy functions. Nevertheless, several techniques and algorithms have been adopted to overcome these challenges, and the last two decades have seen exciting advances in enhanced sampling algorithms, computational power and tertiary structure prediction methodologies. This review aims at summarizing these computational techniques, specifically conformational sampling algorithms and energy approximations that have been frequently used to study protein-folding mechanisms or to de novo predict protein tertiary structures. We hope that this review can serve as an overview on how the protein-folding problem can be studied computationally and, in cases where experimental approaches are prohibitive, help the researcher choose the most relevant computational approach for the problem at hand. We conclude with a summary of current challenges faced and an outlook on potential future directions.
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Registered trials
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