ArticleTheoretical chemistry accounts2011
Trends in template/fragment-free protein structure prediction.
Article in Theoretical chemistry accounts, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- 3 = 1 + 2: how the divide conquered de novo protein structure prediction and what is next?National science review · 2023Article
- Naive Prediction of Protein Backbone Phi and Psi Dihedral Angles Using Deep Learning.Molecules (Basel, Switzerland) · 2023Article
- Secondary structure specific simpler prediction models for protein backbone angles.BMC bioinformatics · 2022Article
- Deep learning for protein secondary structure prediction: Pre and post-AlphaFold.Computational and structural biotechnology journal · 2022Review
- Evolution as a Guide to DesigningInternational journal of molecular sciences · 2021Review
- Enhancing protein backbone angle prediction by using simpler models of deep neural networks.Scientific reports · 2020Article
- Article
- The full dynamics of energy relaxation in large organic molecules: from photo-excitation to solvent heating.Chemical science · 2019Article
- End-to-End Differentiable Learning of Protein Structure.Cell systems · 2019Article
- Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks.Scientific reports · 2018Article
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in bioinformatics · 2018Article
- Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.Scientific reports · 2015Article
- Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome.Proteins · 2014Article
- LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains.Journal of computational chemistry · 2014Article
- SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles.Briefings in bioinformatics · 2013Article
- Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures.The journal of physical chemistry. B · 2012Article
- Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates.Bioinformatics (Oxford, England) · 2011Article
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Authors and funding
5 authors.
Funding
Abstract
Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward.
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Registered trials
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