In another structural assignment method STRIDE, Frischman et al. One of the widely used such methods, DSSP, clusters protein 5-mers into eight classes: Seven of the groups reflect certain structural patterns, such as α-helices, β-sheets, 3/10 helices et.c., and the eighth “blank” group is used if no other structural pattern applies. Secondary structure assignments predominantly exploit hydrogen bond information to group protein fragments. These can be secondary structure-based classifications, as well as classifications based on so-called structural alphabets or protein blocks (PBs). For that reason, many local structure prediction methods rely on these fragments’ classification into certain structural classes. A lot of information can be drawn from the known structures of the fragments with similar characteristics. In the context of local structure prediction, the ultimate goal is to reconstruct the atomic coordinates of a protein fragment as precise as possible, given its amino acid sequence. The predicted structure of local protein fragments serves as a critical component in most global protein folding models, along with homology information and physicochemical properties of amino acids.
YM, AN, YK, VT and NE have been partially supported by the Russian Foundation for Basic Research grant 20-04-01085.Ĭompeting interests: The authors have declared that no competing interests exist.ĭue to fast development of machine learning and statistical inference methods, recent years brought significant progress in protein local structure classification and prediction. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All relevant data are within the manuscript, its Supporting information files and our open repository, which is also referenced in the text of the manuscript.įunding: VM has been partially supported by the DFG FOR 2715. Received: OctoAccepted: ApPublished: May 20, 2021Ĭopyright: © 2021 Milchevskaya et al. (2021) Structural coordinates: A novel approach to predict protein backbone conformation. Citation: Milchevskaya V, Nikitin AM, Lukshin SA, Filatov IV, Kravatsky YV, Tumanyan VG, et al.
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