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Biomolecules, 2023 Determining Secondary Structure Elements (SSEs) for any protein is crucial as an intermediate step for experimental tertiary structure determination. SSEs are identified using popular tools such as DSSP and STRIDE.
Ali Sekmen +4 more
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Protein secondary structure in spider silk nanofibrils
Nature Communications, 2022 Secondary fibril structure is a key component of the mechanical properties of protein materials like silk, yet, limited information is known about the internal structure of these protein fibrils. Here, the authors report on the use of polarised Raman and
Qijue Wang +8 more
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Linkers of secondary structures in proteins [PDF]
Protein Science, 1997 AbstractLinkers that connect repeating secondary structures fall into conformational classes based on distance and main‐chain torsion clustering. A data set of 300 unique protein chains with low pairwise sequence identity was clustered into only a few groups representing the preferred motifs.
V, Geetha, P J, Munson
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Frontiers in Chemistry, 2021 Development of protein 3-D structural comparison methods is important in understanding protein functions. At the same time, developing such a method is very challenging.
Sarika Kondra +3 more
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Biomolecules, 2020 The model of protein folding proposed by Ptitsyn and colleagues involves the accretion of secondary structures around a nucleus. As developed by Efimov, this model also provides a useful way to view the relationships among structures.
William R. Taylor
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BMC Bioinformatics, 2020 Background Whenever suitable template structures are not available, usage of fragment-based protein structure prediction becomes the only practical alternative as pure ab initio techniques require massive computational resources even for very small ...
Jad Abbass, Jean-Christophe Nebel
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Protein Backbone Torsion Angle-Based Structure Comparison and Secondary Structure Database Web Server [PDF]
Genomics & Informatics, 2013 Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural ...
Sunghoon Jung +3 more
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Comparative visualization of protein secondary structures [PDF]
BMC Bioinformatics, 2017 Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein behavior and to design proteins with modified properties.
Lucia Kocincová +5 more
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Discovering the Ultimate Limits of Protein Secondary Structure Prediction
Biomolecules, 2021 Secondary structure prediction (SSP) of proteins is an important structural biology technique with many applications. There have been ~300 algorithms published in the past seven decades with fierce competition in accuracy.
Chia-Tzu Ho +4 more
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Bayesian Segmentation of Protein Secondary Structure [PDF]
Journal of Computational Biology, 2000 We present a novel method for predicting the secondary structure of a protein from its amino acid sequence. Most existing methods predict each position in turn based on a local window of residues, sliding this window along the length of the sequence. In contrast, we develop a probabilistic model of protein sequence/structure relationships in terms of ...
Scott C. Schmidler +2 more
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