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ZENODO
Software . 2026
License: CC BY
Data sources: ZENODO
ZENODO
Software . 2026
License: CC BY
Data sources: Datacite
ZENODO
Software . 2026
License: CC BY
Data sources: Datacite
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S8kPred: A Novel Approach for Protein Secondary Structure Prediction Using 8000 Tripeptide Propensities

Authors: Kumar, Mayank; Rathore, Ravindranath Singh;

S8kPred: A Novel Approach for Protein Secondary Structure Prediction Using 8000 Tripeptide Propensities

Abstract

Accurate prediction of protein secondary structure is essential for reliable tertiary structure prediction and peptide design. To address this, multiple algorithms have been proposed. The conformation of a residue within a polypeptide chain is strongly influenced by its immediate neighbors. The conformational tendencies of 20 residues in the presence of their first neighbors, constituting a total of 8000 tripeptides, were calculated. Using the propensity values of 8000 tripeptide variants, we propose an accurate method for secondary structure prediction. Various machine learning (ML) models were built using propensities, position-specific scoring matrices (PSSM) and amino acid binary features to predict three-state (Q3) and eight-state (Q8) secondary structures. The results suggest that the XGBoost ML model produced highly accurate predictions, achieving accuracies of 93% and 88% for Q3 and Q8 state, respectively for validation dataset CB513. A program for prediction called S8kPred is developed. This utility along with consensus secondary structure prediction is available online at https://www.s8kpred.in.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average