ArticleBMC structural biology2014
A three dimensional visualisation approach to protein heavy-atom structure reconstruction.
Article in BMC structural biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Kinematic Reconstruction of Cyclic Peptides and Protein Backbones from Partial Data.Journal of chemical information and modeling · 2021Article
- On topology and knotty entanglement in protein folding.PloS one · 2021Article
- Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example.PloS one · 2021Article
- Study of correlations between protein peptide plane dynamics and side chain dynamics.PloS one · 2019Article
- A distance geometry-based description and validation of protein main-chain conformation.IUCrJ · 2017Article
- A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning.Journal of proteomics & bioinformatics · 2016Article
- Clustering and percolation in protein loop structures.BMC structural biology · 2015Article
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Authors and funding
5 authors.
Funding
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Abstract
backgroundA commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates.
resultsWe employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the Cα coordinates. Each heavy atom is visualised on the surfaces of a different two-sphere, that is centered at another heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters, that display a clear and strong dependence on the underlying backbone secondary structure.
conclusionsWe demonstrate that there is a clear interdependence between rotameric states and secondary structure. Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage. Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.
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