ArticleNature communications2022
Helical structure motifs made searchable for functional peptide design.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 25 citations in OpenAlex.
- Self-assembling protein nanoparticles for cytosolic delivery of nucleic acids and proteins.Nature biotechnology · 2026Article
- AI-assisted design of a VEGFR2 agonistic peptide that promotes angiogenesis and wound repair.Protein science : a publication of the Protein Society · 2026Article
- Peptide cages: bioinspired supramolecular architectures for next-generation applications.Chemical science · 2026Review
- Antimicrobial peptides: structure, functions and translational applications.Nature reviews. Microbiology · 2025Review
- Rational Design of PCR12mod6, a Cathelicidin-HR-Derived Peptide with Enhanced Dual-Action Antimicrobial and Antioxidant Activity.ACS omega · 2025Article
- Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models.ACS omega · 2024Article
- Design and evaluation of tadpole-like conformational antimicrobial peptides.Communications biology · 2023Article
- Synthetic extracellular matrices with function-encoding peptides.Nature reviews bioengineering · 2023Review
- Probing local changes to α-helical structures with 2D IR spectroscopy and isotope labeling.Biophysical journal · 2023Article
- Accelerated NLRP3 inflammasome-inhibitory peptide design using a recurrent neural network model and molecular dynamics simulations.Computational and structural biotechnology journal · 2023Article
- The Role ofInternational journal of molecular sciences · 2022Review
- Design of Protein Segments and Peptides for Binding to Protein Targets.Biodesign research · 2022Review
Corrections and comments
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Authors and funding
21 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/ .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.