Dbaasp : Database of Antimicrobial Activity and Structure of Peptides (original) (raw)
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Dbaasp: Database of Antimicrobial Activity and Structure of Peptides
Fems Microbiology Letters, 2014
The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is a manually curated database for those peptides for which antimicrobial activity against particular targets has been evaluated experimentally. The database is a depository of complete information on: the chemical structure of peptides; target species; target object of cell; peptide antimicrobial/haemolytic/cytotoxic activities; and experimental conditions at which activities were estimated. The DBAASP search page allows the user to search peptides according to their structural characteristics, complexity type (monomer, dimer and two-peptide), source, synthesis type (ribosomal, nonribosomal and synthetic) and target species. The database prediction algorithm provides a tool for rational design of new antimicrobial peptides. DBAASP is accessible at http://www.biomedicine.org. ge/dbaasp/.
Nucleic Acids Research
The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures, bioactivities and toxicities of peptides that possess antimicrobial properties. DBAASP is updated continuously, and at present, version 3.0 (DBAASP v3) contains >15 700 entries (8000 more than the previous version), including >14 500 monomers and nearly 400 homo- and hetero-multimers. Of the monomeric antimicrobial peptides (AMPs), >12 000 are synthetic, about 2700 are ribosomally synthesized, and about 170 are non-ribosomally synthesized. Approximately 3/4 of the entries were added after the initial release of the database in 2014 reflecting the recent sharp increase in interest in AMPs. Despite the increased interest, adoption of peptide antimicrobials in clinical practice is still limited as a consequence of several factors including side effects, problems with bioavailab...
Nucleic acids research, 2015
Antimicrobial peptides (AMPs) are anti-infectives that may represent a novel and untapped class of biotherapeutics. Increasing interest in AMPs means that new peptides (natural and synthetic) are discovered faster than ever before. We describe herein a new version of the Database of Antimicrobial Activity and Structure of Peptides (DBAASPv.2, which is freely accessible at http://dbaasp.org). This iteration of the database reports chemical structures and empirically-determined activities (MICs, IC50, etc.) against more than 4200 specific target microbes for more than 2000 ribosomal, 80 non-ribosomal and 5700 synthetic peptides. Of these, the vast majority are monomeric, but nearly 200 of these peptides are found as homo- or heterodimers. More than 6100 of the peptides are linear, but about 515 are cyclic and more than 1300 have other intra-chain covalent bonds. More than half of the entries in the database were added after the resource was initially described, which reflects the rece...
Concerns in the Design and Development of Novel Antimicrobial Peptides
2017
Peptide and protein based therapeutics are the most promising approaches in today medicine. Bioactive peptides can be valuable drugs in the treatment of various illnesses, such as cardiovascular and neurodegenerative diseases. Cell toxic peptides can be considered for cancer or infection therapy. Antimicrobial peptides (AMPs) are one of the most interesting antibiotic groups in this regard, especially in drug resistance infections. Numerous AMPs have been discovered from the natural source; however, artificial synthetic ones have been also developed based on rational design or bioinformatics modeling. Physicochemical features of AMPs are highly important in their antibacterial activity as well as their toxicity. The best AMP is the one that has selective potent antimicrobial bioactivity and no or least hemolytic and cytotoxic effect. In this review, various structural factors affecting the AMPs bioactivity, such as AMPs size, charge, amphipathicity, and amino acid sequence are illus...
CAMP: a useful resource for research on antimicrobial peptides
Nucleic Acids Research, 2010
Antimicrobial peptides (AMPs) are gaining popularity as better substitute to antibiotics. These peptides are shown to be active against several bacteria, fungi, viruses, protozoa and cancerous cells. Understanding the role of primary structure of AMPs in their specificity and activity is essential for their rational design as drugs. Collection of Anti-Microbial Peptides (CAMP) is a free online database that has been developed for advancement of the present understanding on antimicrobial peptides. It is manually curated and currently holds 3782 antimicrobial sequences. These sequences are divided into experimentally validated (patents and non-patents: 2766) and predicted (1016) datasets based on their reference literature. Information like source organism, activity (MIC values), reference literature, target and non-target organisms of AMPs are captured in the database. The experimentally validated dataset has been further used to develop prediction tools for AMPs based on the machine learning algorithms like Random Forests (RF), Support Vector Machines (SVM) and Discriminant Analysis (DA). The prediction models gave accuracies of 93.2% (RF), 91.5% (SVM) and 87.5% (DA) on the test datasets. The prediction and sequence analysis tools, including BLAST, are integrated in the database. CAMP will be a useful database for study of sequence-activity and -specificity relationships in AMPs. CAMP is freely available at
Antimicrobial Peptides: An Update on Classifications and Databases
International Journal of Molecular Sciences
Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.
In Silico Studies in Antimicrobial Peptides Design and Development
IOP conference series, 2019
Antimicrobial peptides (AMPs) are a group of natural-derived molecules exhibited broad spectrum antimicrobial activity. Currently these molecules have been investigated comprehensively due to their interesting features regarding antimicrobial and immunomodulatory mode of actions which placed them as promising therapeutics agents in this post antibiotics era. Numerous strategies have been implemented in order to develop a novel AMP for biotechnology and therapeutics applications, one of which is in silico study.. This approach offers a rapid and cost effective manner in AMPs design and development. In silico studies provide additional and substantial information for in vitro techniques. In this paper, we deliver an overview of the applicable in silico approaches that have been used in designing and developing AMPs.
Antibacterial Activity of Rationally Designed Antimicrobial Peptides
International Journal of Microbiology
Many infectious diseases are still prevalent in the world’s populations since no effective treatments are available to eradicate them. The reasons may either be the antibiotic resistance towards the available therapeutic molecules or the slow rate of producing adequate therapeutic regimens to tackle the rapid growth of new infectious diseases, as well as the toxicity of current treatment regimens. Due to these reasons, there is a need to seek and develop novel therapeutic regimens to reduce the rapid scale of bacterial infections. Antimicrobial Peptides (AMPs) are components of the first line of defense for prokaryotes and eukaryotes and have a wide range of activities against Gram-negative and Gram-positive bacteria, fungi, cancer cells, and protozoa, as well as viruses. In this study, peptides which were initially identified for their HIV inhibitory activity were further screened for antibacterial activity through determination of their kinetics as well as their cytotoxicity. From...
Bacterial drug resistance has become a serious problem worldwide as a consequence of long-term use and misuse of antibiotics. Current research trends indicate the development of anti-microbial peptides (AMPs) as a promising alternative to conventional antibiotics and to tackle antibiotic resistance. In the present work, novel short AMPs containing less than 15 amino acids with potential broad-spectrum activity are de-novo designed. A computational database-guided pipeline of rational analysis and modification is developed and utilized based on established principles of AMP activity such as charge, hydrophobicity, length, amino-acid frequency, charge density and hydrophobic moments. Potential broad-spectrum AMP sequences are designed based on a consecutive refinement strategy in which seed AMP sequences with desirable properties are predicted from scratch and then modified for possible improvement inactivity. Finally, four AMP sequences were designed, synthesized and tested for their efficacy in-vitro for broad spectrum anti-microbial activity against major drug resistant pathogens namely two Gram-positive organisms Staphylococcus aureus, Bacillus cereus and two Gram-negative pathogens Klebsiella aerogenes and Klebsiella pnuemoniae. Based on the inhibitory concentrations, two among the four designed peptides namely PEP01 (GKIMYILTKKS) and PEP03 (FGIKLRSVWKR) showed best results as broad-spectrum AMPs among which the sequence of PEP03 is further projected as a better candidate in terms of its predicted cell-penetrating and non-toxic nature.