Welcome to the official repository and documentation overview for SAPdb, the first dedicated repository of short peptides (dipeptides and tripeptides) that undergo self-assembly to form well-defined ordered nanostructures. This resource is designed to help researchers in nanobiotechnology understand the mechanisms and experimental conditions governing the formation of peptide-based nanomaterials.
Web Server: https://webs.iiitd.edu.in/raghava/sapdb/
Mathur, D., Kaur, H., Dhall, A., Sharma, N., & Raghava, G. P. S. (2021). SAPdb: A database of short peptides and the corresponding nanostructures formed by self-assembly. Computers in Biology and Medicine, 133, 104391. https://doi.org/10.1016/j.compbiomed.2021.104391
This dataset can also be found on Zenodo at https://doi.org/10.5281/zenodo.20078457
SAPdb was developed to provide a systematic collection of experimental data for the burgeoning field of peptide nanobiotechnology. Short peptides, specifically di- and tripeptides, are ideal building blocks for nanomaterials due to their low toxicity, cost-efficiency, and ease of synthesis. SAPdb consolidates scattered literature into a single platform to facilitate the rational design of diverse nanostructures.
The database integrates data from:
- Primary Literature: 1,049 entries manually curated from 301 research articles.
- Experimental Data: Focused on validated nanostructures including nanofibers, nanotubes, nanorods, and hydrogels.
- 1,049 Unique Entries: Detailed records of self-assembling short peptides.
- Peptide Classification: Includes 701 dipeptides, 328 tripeptides, and 20 single amino acids with conjugate partners.
- Diverse Modifications: Covers sequences containing D-amino acids, non-natural residues, and various chemical modifications.
Each record includes:
- Structural Details: Specific type of nanostructure formed (e.g., nanosphere, nanoparticle, hydrogel).
- Experimental Conditions: Critical parameters such as pH, temperature, solvent, and concentration required for self-assembly.
- Chemical Properties: Sequence modifications and aromaticity, which often favor self-assembly.
- Therapeutic Potential: Insights into applications such as drug delivery, tissue engineering, and biosensors.
- Search Modules: User-friendly tools for querying the database by peptide sequence, modification, or nanostructure type.
- Browsing Facility: Classified browsing by peptide length, conformation, and chemical modifications.
- Analysis Tools: Integrated modules to examine how substitutions (like D-amino acids) influence the bottom-up self-assembly process.
SAPdb is structured to provide a comprehensive look at the "bottom-up" process of nanostructure formation:
- Peptide Information: Core data including amino acid sequence and chemical modifications.
- Assembly Conditions: Detailed documentation of the environment (pH, solvent) that triggers self-assembly.
- Morphology: Classification of the resulting nanomaterial, from 1D fibers to 3D hydrogels.
- Drug Delivery: Designing peptide nanocarriers that improve uptake by targeted cells while maintaining low cytotoxicity.
- Biomedical Engineering: Developing building blocks for hydrogels and scaffolds used in cell culture and tissue engineering.
- Material Science: Using short peptides as models for nanofabrication, bioelectronics, and diagnostic biosensors.
Prof. G.P.S. Raghava raghava@iiitd.ac.in Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi), New Delhi, India.
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