ArticleNucleic acids research2009
NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
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- Navigating Homogeneous Graph Paths Through Amyloidogenic and Non-Amyloidogenic Hexapeptides.Journal of computational chemistry · 2025Article
- Prediction and Evaluation of Protein Aggregation with Computational Methods.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Enhancing protein aggregation prediction: a unified analysis leveraging graph convolutional networks and active learning.RSC advances · 2024Article
- DOTAD: A Database of Therapeutic Antibody Developability.Interdisciplinary sciences, computational life sciences · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Stabilization challenges and aggregation in protein-based therapeutics in the pharmaceutical industry.RSC advances · 2023Review
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- AB-Amy: machine learning aided amyloidogenic risk prediction of therapeutic antibody light chains.Antibody therapeutics · 2023Article
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- Succinct Amyloid and Nonamyloid Patterns in Hexapeptides.ACS omega · 2022Article
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- NAMPT Inhibitor and P73 Activator Represses P53 R175H Mutated HNSCC Cell Proliferation in a Synergistic Manner.Biomolecules · 2022Article
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- Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- ReRF-Pred: predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition.BMC bioinformatics · 2021Article
- Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles.Molecules (Basel, Switzerland) · 2021Article
- The Budapest Amyloid Predictor and Its Applications.Biomolecules · 2021Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The calculation of contact-dependent secondary structure propensity (CSSP) is a unique and sensitive method that detects non-native secondary structure propensities in protein sequences. This method has applications in predicting local conformational change, which typically is observed in core sequences of protein aggregation and amyloid fibril formation. NetCSSP implements the latest version of the CSSP algorithm and provides a Flash chart-based graphic interface that enables an interactive calculation of CSSP values for any user-selected regions in a given protein sequence. This feature also can quantitatively estimate the mutational effect on changes in native or non-native secondary structural propensities in local sequences. In addition, this web tool provides precalculated non-native secondary structure propensities for over 1,400,000 fragments that are seven-residues long, collected from PDB structures. They are searchable for chameleon subsequences that can serve as the core of amyloid fibril formation. The NetCSSP web tool is available at http://cssp2.sookmyung.ac.kr/.
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