ArticleJournal of computational chemistry2014
PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Droplet growth, Ostwald's rule, and emergence of order in Fused in Sarcoma.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- DSSP 4: FAIR annotation of protein secondary structure.Protein science : a publication of the Protein Society · 2025Article
- Mathematical and Machine Learning Approaches for Classification of Protein Secondary Structure Elements fromBiomolecules · 2023Article
- Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.Journal of chemical theory and computation · 2023Article
- Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2022Article
- Automated Protein Secondary Structure Assignment from CBiomolecules · 2022Article
- Assigning secondary structure in proteins using AI.Journal of molecular modeling · 2021Article
- Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models.Small (Weinheim an der Bergstrasse, Germany) · 2017Article
- Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling.Journal of the American Chemical Society · 2016Article
- A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.International journal of molecular sciences · 2016Article
- Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models.Journal of chemical theory and computation · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Proteins are often characterized in terms of their primary, secondary, tertiary, and quaternary structure. Algorithms such as define secondary structure of proteins (DSSP) can automatically assign protein secondary structure based on the backbone hydrogen-bonding pattern. However, the assignment of secondary structure elements (SSEs) becomes a challenge when only the Cα coordinates are available. In this work, we present protein C-alpha secondary structure output (PCASSO), a fast and accurate program for assigning protein SSEs using only the Cα positions. PCASSO achieves ∼95% accuracy with respect to DSSP and takes ∼0.1 s using a single processor to analyze a 1000 residue system with multiple chains. Our approach was compared with current state-of-the-art Cα-based methods and was found to outperform all of them in both speed and accuracy. A practical application is also presented and discussed.
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Registered trials
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