Source AMP Databases
An overview of the key resources used to create the MarLys AMP database
Database Integration
Antimicrobial peptide (AMP) databases are crucial tools supporting research on their properties, structure, and function. They provide quick access to data such as amino acid sequences, biological sources, physicochemical properties, and three-dimensional peptide structures. This data comes from scientific literature, databases like UniProt and NCBI, and experimental results.
To ensure the highest quality and comprehensiveness of our database, we have carefully selected and analyzed existing resources. Below, we present the databases that formed the foundation of our project. Each contributed a unique dataset, allowing us to create a universal and reliable tool for further research.
Description of Used Databases
A brief characterization of each database that contributed to the creation of MarLys AMP
A carefully selected resource aimed at supplementing the limitations of existing databases in antimicrobial research. It contains extensive information on 59,122 AMPs from 18,240 unique sources.
One of the first databases of natural antimicrobial peptides. It contains information on the sequences and activities of peptides from various organisms. Peptides are classified according to their biological properties.
Focuses on peptides tested against biofilms, providing verified experimental data. The database concentrates on peptides active against biofilms.
A database that collects data on AMP sequences, their origin, and biological activity, including synthetic AMPs. It covers both natural and synthetic peptides.
A database of anticancer peptides and proteins. It offers detailed data on their activity, 3D structure, and associated cell lines. It includes not only natural peptides but also those containing chemically modified amino acids.
Provides data on cyclic proteins, supporting research on their structures and functions. It is a database dedicated to cyclic protein sequences and structures, applicable to protein discovery and engineering.
Collects data on antimicrobial peptides, focusing on precursor sequences and their bioactive fragments. It is a database of anuran defense peptides.
Collects data on antimicrobial peptides, providing information on their structures, operating conditions, and molecular targets. It also includes predictive tools to aid in peptide design.
A comprehensive database containing information on antimicrobial peptides, including their sequences, biological activity, post-translational modifications (PTMs), structure, and physicochemical properties.
A database containing peptides with defined sequences, divided into general and patent collections, with data on toxicity and hemolytic activity.
Focuses on peptides derived from invertebrates, offering data on sequences, structures, and physicochemical properties.
Specializes in anti-protozoan peptides, offering information on their structures and mechanisms of action.
Contains data on therapeutic peptides, allowing for sequence and structure similarity searches. It is a database of structurally annotated therapeutic peptides.
Bibliography
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Mondal, R. K., Sen, D., Arya, A., & Samanta, S. K. (2023). Developing anti-microbial peptide database version 1 to provide comprehensive and exhaustive resource of manually curated AMPs. Scientific Reports, 13, 17843. https://doi.org/10.1038/s41598-023-45097-4
Wang, G., Li, X., & Wang, Z. (2016). APD3: The Antimicrobial Peptide Database as a Tool for Research and Education. Nucleic Acids Research, 44(D1), D1087–D1093. https://doi.org/10.1093/nar/gkv1278
Di Luca, M., Maccari, G., Maisetta, G., & Batoni, G. (2015). BaAMPs: The database of biofilm-active antimicrobial peptides. Biofouling, 31(2), 193–199. https://doi.org/10.1080/08927014.2015.1021243
Gawde, U., Chakraborty, S., Waghu, F. H., Barai, R. S., Khanderkar, A., Indraguru, R., Shirsat, T., & Idicula-Thomas, S. (2023). CAMPR4: A database of natural and synthetic antimicrobial peptides. Nucleic Acids Research, 51(D1), D377–D383. https://doi.org/10.1093/nar/gkac953
Yagi, A., Tuknait, A., Anand, P., Gupta, S., Sharma, M., Mathur, D., ... & Raghava, G. P. (2015). CancerPPD: a database of anticancer peptides and proteins. Nucleic Acids Research, 43(D1), D837–D843. https://doi.org/10.1093/nar/gku892
Wang, C. K. L., Kaas, Q., Chiche, L., & Craik, D. J. (2008). CyBase: A database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Research, 36(Database issue), D206–D210. https://doi.org/10.1093/nar/gkm935
Novković, M., Simunić, J., Bojović, V., Tossi, A., & Juretić, D. (2012). DADP: the database of anuran defense peptides. Bioinformatics, 28(10), 1406–1407. https://doi.org/10.1093/bioinformatics/bts173
Pirtskhalava, M., Amstrong, A. A., Grigolava, M., Chubinidze, M., Alimbarashvili, E., Vishnepolsky, B., Gabrielian, A., Rosenthal, A., Hurt, D. E., & Tartakovsky, M. (2021). DBAASP v3: Database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics. Nucleic Acids Research, 49(D1), D288–D297. https://doi.org/10.1093/nar/gkaa1053
Shi, G., Kang, X., Dong, F., Liu, Y., Zhu, N., Hu, Y., Xu, H., Lao, X., & Zheng, H. (2022). DRAMP 3.0: An enhanced comprehensive data repository of antimicrobial peptides. Nucleic Acids Research, 50(D1), D488–D496. https://doi.org/10.1093/nar/gkab1037
Gómez, E. A., Giraldo, P., & Orduz, S. (2017). InverPep: A database of invertebrate antimicrobial peptides. Journal of Global Antimicrobial Resistance, 8, 13–17. https://doi.org/10.1016/j.jgar.2016.11.006
Mehta, D., Anand, P., Kumar, V., Joshi, A., Mathur, D., Singh, S., Tuknait, A., Chaudhary, K., Gautam, S. K., Gautam, A., et al. (2014). ParaPep: A web resource for experimentally validated antiparasitic peptide sequences and their structures. Database, 2014, bau051. https://doi.org/10.1093/database/bau051
Singh, S., Chaudhary, K., Dhanda, S. K., Bhalla, S., Usmani, S. S., Gautam, A., Tuknait, A., Agrawal, P., Mathur, D., & Raghava, G. P. S. (2016). SATPdb: A database of structurally annotated therapeutic peptides. Nucleic Acids Research, 44(D1), D1119–D1126. https://doi.org/10.1093/nar/gkv1292