Results 1 to 10 of about 955,526 (247)

Mathematical and Machine Learning Approaches for Classification of Protein Secondary Structure Elements from Cα Coordinates

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, Kamal Al Nasr, Bahadir Bilgin, Ahmet Bugra Koku, Christopher Jones   +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, Patrick McArdle, Stephanie L. Wang, Ryan L. Wilmington, Zhen Xing, Alexander Greenwood, Myriam L. Cotten, M. Mumtaz Qazilbash, Hannes C. Schniepp   +8 more
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Exploring Protein Fold Space

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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Development of a TSR-Based Method for Protein 3-D Structural Comparison With Its Applications to Protein Classification and Motif Discovery

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, Titli Sarkar, Vijay Raghavan, Wu Xu   +3 more
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Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure

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, Se-Eun Bae, Insung Ahn, Hyeon S. Son   +3 more
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A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction.

PLoS ONE, 2021
Protein secondary structure prediction (SSP) has a variety of applications; however, there has been relatively limited improvement in accuracy for years.
Teng-Ruei Chen, Sheng-Hung Juan, Yu-Wei Huang, Yen-Cheng Lin, Wei-Cheng Lo   +4 more
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Secondary structure determines protein topology [PDF]

Protein Science, 2006
AbstractUsing a test set of 13 small, compact proteins, we demonstrate that a remarkably simple protocol can capture native topology from secondary structure information alone, in the absence of long‐range interactions. It has been a long‐standing open question whether such information is sufficient to determine a protein's fold.
Patrick J, Fleming, Haipeng, Gong, George D, Rose   +2 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.
Kocincova, Lucia, Jaresova, Miroslava, Byska, Jan, Parulek, Julius, Hauser, Helwig, Kozlikova, Barbora   +5 more
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PS4: a next-generation dataset for protein single-sequence secondary structure prediction

BioTechniques, 2023
Protein secondary structure prediction is a subproblem of protein folding. A light-weight algorithm capable of accurately predicting secondary structure from only the protein residue sequence could provide useful input for tertiary structure prediction ...
Omar Peracha
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