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Properties and Origins of Protein Secondary Structure [PDF]
Phys. Rev. E 49 (1994) 3440, 1994 Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain. Using this definition and a simple model for proteins, the forces driving the formation of secondary structure are ...
Nicholas D. Socci +5 more
arxiv +5 more sources
Protein secondary structure: Entropy, correlations and prediction [PDF]
Bioinformatics, 2003 Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions?
Brenner, Steven E., Crooks, Gavin E.
core +10 more sources
Fourier-based classification of protein secondary structures [PDF]
Biochemical and Biophysical Research Communications, Vol. 485, No.
4, pp. 731-735, 2017, 2017 The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications.
Shu, Jian-Jun, Yong, Kian Yan
arxiv +6 more sources
Solvent Effects on the Secondary Structures of Proteins [PDF]
The Journal of Physical Chemistry A, 1999 We examined the effect of solvation on the conformational preferences (e.g., α-helix versus β-sheet) of tripeptides using ab initio quantum mechanics (Hartree−Fock 6-31G**) with solvation in the Poisson−Boltzmann continuum solvent approximation. We find that aqueous solvent preferentially stabilizes the α-helix conformation over β-sheet conformations ...
Changmoon Park +2 more
openalex +5 more sources
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
doaj +1 more source
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
doaj +1 more source
Protein Secondary Structure Prediction With a Reductive Deep Learning Method
Frontiers in Bioengineering and Biotechnology, 2021 Protein secondary structures have been identified as the links in the physical processes of primary sequences, typically random coils, folding into functional tertiary structures that enable proteins to involve a variety of biological events in life ...
Zhiliang Lyu +5 more
doaj +1 more source
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
doaj +1 more source
Frontiers in Bioengineering and Biotechnology, 2021 Alpha transmembrane proteins (αTMPs) profoundly affect many critical biological processes and are major drug targets due to their pivotal protein functions.
Zhe Liu +7 more
doaj +1 more source
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.
P. J. Munson, V. Geetha
openaire +3 more sources