Pervasive, conserved secondary structure in highly charged protein regions.
PLoS Computational Biology, 2023 Understanding how protein sequences confer function remains a defining challenge in molecular biology. Two approaches have yielded enormous insight yet are often pursued separately: structure-based, where sequence-encoded structures mediate function, and
Catherine G Triandafillou +3 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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Extracting Physicochemical Features to Predict Protein Secondary Structure
The Scientific World Journal, 2013 We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass.
Yin-Fu Huang, Shu-Ying Chen
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Convolution-Bidirectional Temporal Convolutional Network for Protein Secondary Structure Prediction
IEEE Access, 2022 As a basic feature extraction method, convolutional neural networks have some information loss problems when dealing with sequence problems, and a temporal convolutional network can compensate for this problem.
Yunqing Zhang, Yuming Ma, Yihui Liu
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An evolutionary method for learning HMM structure: prediction of protein secondary structure
BMC Bioinformatics, 2007 Background The prediction of the secondary structure of proteins is one of the most studied problems in bioinformatics. Despite their success in many problems of biological sequence analysis, Hidden Markov Models (HMMs) have not been used much for this ...
Won Kyoung-Jae +3 more
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Motivated proteins: a web application for studying small three-dimensional protein motifs [PDF]
, 2009 <b>BACKGROUND:</b> Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and ...
Milner-White, E.J. +5 more
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The CATH database: an extended protein family resource for structural and functional genomics [PDF]
, 2003 The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34 287 domain structures classified into 1383 superfamilies and 3285 sequence families.
Pearl, F.M.G. +8 more
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Protein Secondary Structure Affects Glycan Clustering in Native Mass Spectrometry
Life, 2021 Infection by the human noroviruses (hNoV), for the vast majority of strains, requires attachment of the viral capsid to histo blood group antigens (HBGAs).
Hao Yan +8 more
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Structural analysis of Salmonella enterica effector protein SopD [PDF]
, 2004 Salmonella outer protein D (SopD) is a type III secreted virulence effector protein from Salmonella enterica. Full-length SopD and SopD lacking 16 amino acids at the N-terminus (SopDDeltaN) have been expressed as fusions with GST in Escherichia coli ...
Williams, C +7 more
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International Journal of Food Properties, 2022 Fish protein hydrolyzates (FPH) are breakdown products of hydrolysis and are gaining importance in the field of nutraceuticals and functional foods due to their bioactive properties, high nutritional value, solubility, and digestibility. This study aimed
Undiganalu Gangadharappa Yathisha +2 more
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