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. 2016 Jan 4;44(D1):D1104-12.
doi: 10.1093/nar/gkv1174. Epub 2015 Nov 17.

DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides

Malak Pirtskhalava  1 , Andrei Gabrielian  2 , Phillip Cruz  2 , Hannah L Griggs  2 , R Burke Squires  2 , Darrell E Hurt  2 , Maia Grigolava  3 , Mindia Chubinidze  3 , George Gogoladze  3 , Boris Vishnepolsky  3 , Vsevolod Alekseyev  2 , Alex Rosenthal  2 , Michael Tartakovsky  2
Affiliations

DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides

Malak Pirtskhalava et al. Nucleic Acids Res. .

Erratum in

Abstract

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 recent sharp uptick of interest in AMPs. New features of DBAASPv.2 include: (i) user-friendly utilities and reporting functions, (ii) a 'Ranking Search' function to query the database by target species and return a ranked list of peptides with activity against that target and (iii) structural descriptions of the peptides derived from empirical data or calculated by molecular dynamics (MD) simulations. The three-dimensional structural data are critical components for understanding structure-activity relationships and for design of new antimicrobial drugs. We created more than 300 high-throughput MD simulations specifically for inclusion in DBAASP. The resulting structures are described in the database by novel trajectory analysis plots and movies. Another 200+ DBAASP entries have links to the Protein DataBank. All of the structures are easily visualized directly in the web browser.

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Figures

Figure 1.
Figure 1.
Distribution of the length of the peptides in DBAASP v.2.
Figure 2.
Figure 2.
Difference between frequencies of occurrence of amino acids in DAASPv.2 and in UniProt: (A) difference between Ribosomal peptides from DBAASP and UniProt; (B) difference between Synthetic peptides from DBAASP and UniProt.
See this image and copyright information in PMC

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