CAMPR4: a database of natural and synthetic antimicrobial peptides

Abstract

There has been an exponential increase in the design of synthetic antimicrobial peptides (AMPs) for its use as novel antibiotics. Synthetic AMPs are substantially enriched in residues with physicochemical properties known to be critical for antimicrobial activity; such as positive charge, hydrophobicity, and higher alpha helical propensity. The current prediction algorithms for AMPs have been developed using AMP sequences from natural sources and hence do not perform well for synthetic peptides. In this version of CAMP database, along with updating sequence information of AMPs, we have created separate prediction algorithms for natural and synthetic AMPs. CAMPR4 holds 24243 AMP sequences, 933 structures, 2143 patents and 263 AMP family signatures. In addition to the data on sequences, source organisms, target organisms, minimum inhibitory and hemolytic concentrations, CAMPR4 provides information on N and C terminal modifications and presence of unusual amino acids, as applicable. The database is integrated with tools for AMP prediction and rational design (natural and synthetic AMPs), sequence (BLAST and clustal omega), structure (VAST) and family analysis (PRATT, ScanProsite, CAMPSign). The data along with the algorithms of CAMPR4 will aid to enhance AMP research. CAMPR4 is accessible at http://camp.bicnirrh.res.in/.

Designing Cell Delivery Peptides and SARS-CoV-2-Targeting Small Interfering RNAs: A Comprehensive Bioinformatics Study with Generative Adversarial Network-Based Peptide Design and In Vitro Assays

“…Additionally, as the work by Tucs et al . on AMPs (PepGAN) showed that most of their new peptides were cationic and amphiphilic, and to enrich the training sets for GAN, sequences from their data sets (retrieved from Antimicrobial Peptide Database (APD), Collection of Anti-Microbial Peptides (CAMP), Linking Antimicrobial Peptides (LAMP), and Database of Antimicrobial Activity and Structure of Peptides (DBAASP) databases) were also collected. Sequences with up to 52 amino acids were used for training, and redundant sequences were removed.…”

Analysis, Modeling, and Target-Specific Predictions of Linear Peptides Inhibiting Virus Entry

“…Various resources have been employed to offer information and sequences of AVPs. ,− However, DBAASP stands out, as it presents the annotation of the virus entry inhibitory activity in the most user-friendly and convenient form. Therefore, target viruses were chosen from DBAASP or from the literature, and information on sequences and structures of the envelope proteins was acquired from Uniprot, PDB Bank, and Genbank …”

Protective Barriers Provided by the Epidermis

“…More than 3000 naturally occurring antimicrobial peptides have been identified, and there is a database containing 24,243 natural and synthetic antimicrobial peptides [ 106 ]. More than 60 antimicrobial peptides have been approved by the FDA [ 107 ]. The natural antimicrobial peptides are susceptible to proteolytic degradation and are hemolytic [ 108 , 109 ].…”