README.md

metadata

pretty_name: Peptide Designer Data
license: other
tags:
  - peptides
  - antimicrobial-peptides
  - gtm
  - wasserstein-autoencoder
  - safetensors
  - parquet

Peptide Designer Data

This dataset contains structured, aggregate GTM landscape assets for peptide design. The primary bundle is landscapes/dbaasp_amp_v1/.

Raw DBAASP records and raw peptide source datasets are not redistributed. The bundle contains node-level aggregate tensors, aggregate Parquet tables, plots, metadata, and a compressed GTM runtime pickle for agent sampling.

Decoder

Compatible peptide decoder: axelrolov/wae_peptides.

Landscape Bundle

• landscape.json: machine-readable landscape contract
• landscape.safetensors: dense GTM and aggregate landscape arrays
• nodes.parquet: aggregate node-level activity/density records
• sampler.json: default sampling policy
• plots/: rendered HTML plots
• plots/organisms/<organism>/: separate ChemographyKit Altair density/activity landscapes and Plotly active-probability HTML/PNG landscapes
• plots/images/: static image artifacts
• runtime/gtm.pkl.gz: compressed GTM/scaler/config pickle for trusted agent sampling workflows

Activity organisms included: 16.

Source and Attribution

Data were obtained from the DBAASP (https://dbaasp.org) which is an open-access AMP data resource supported by I. Beritashvili Center of Experimental Biomedicine (IBCEB), Tbilisi, Georgia and the National Institute of Allergy and Infectious Diseases (NIAID) Office of Cyber Infrastructure and Computational Biology (OCICB) in Bethesda, MD. These data were collected and submitted by members of the DBAASP team.

Please cite:

Pirtskhalava M, Amstrong AA, Grigolava M, Chubinidze M, Alimbarashvili E, Vishnepolsky B, Gabrielian A, Rosenthal A, Hurt DE, Tartakovsky M. DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D288-D297, https://doi.org/10.1093/nar/gkaa991