Structural biologists are at last living the dream of visualizing macromolecules to uncover their function. But it means integrating different technologies, and that's no easy feat.
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Ornes, S. Let the structural symphony begin. Nature 536, 361–363 (2016). https://doi.org/10.1038/536361a
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DOI: https://doi.org/10.1038/536361a
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Nature Methods (2017)
Carlos Polanco
To the editor:
Protein function & con formal mappings
Stephen Ornes (1) [Let the structural symphony begin, Nature] discusses the present, and future possibilities for identification of the protein function using current technologies.
Different bioinformatics algorithms (2-5) restrict the functional protein prediction only to the linear sequence. In my view, it is important to explore this scientific approach and review the physico-chemical metrics used taking advantage of currently available software to visualize the results in 3D-space. From the linear sequence derives the three-dimensional protein conformation, therefore, there must be a non-linear transformation (in the mathematical sense) that generates a subspace with a single physico-chemical property. Of course, this statement has to be demonstrated, but if this assumption is true, it would substantially reduce the functional protein identification process.
Sincerely,
Carlos Polanco, Ph.D., D.Sc.
Universidad Nacional Autónoma de México, México City, México.
Carlos Polanco is Associate Professor at the Department of Mathematics, at Universidad Nacional Autónoma de México. México City, México. (polanco@unam.mx)
References
1. Ornes S. Let the structural symphony begin. Nature 2016: 361?363 DOI:10.1038/536361a.
2. Vilar S, Costanzi S. Predicting Biological Activities through QSAR Analysis and Docking-based Scoring. Methods in molecular biology (Clifton, NJ). 2012914:271-284. doi:10.1007/978-1-62703-023-6_16.
3. Yang Y, Li Y, Pan Y, et al. Computational Analysis of Structure-Based Interactions for Novel H1-Antihistamines. González-Díaz H, ed. International Journal of Molecular Sciences. 2016;17(1):129. doi:10.3390/ijms17010129.
4. Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Computational Methods in Drug Discovery. Barker EL, ed. Pharmacological Reviews. 2014;66(1):334-395. doi:10.1124/pr.112.007336.
5. Polanco C, Buhse T, Uversky VN. Structure and function relationships of proteins based on polar profile: a review. Acta Biochim Pol. 2016;63(2):229-33. doi: 10.18388/abp.2014_919.