Skip to content
PocketVina Atlas

What's new

· Preview build

  • "Best" is now "highest affinity" everywhere on the site: it only ever meant the lowest Vina score. File and field names keep "best"; the API page says what it means.
  • The 3D view sits at the page width again, viewer and panel side by side; full screen is one click away.
  • Pocket buttons: the pocket shown is filled, here and under the viewer; ★ marks the pocket with the highest-affinity pose.
  • PoseBusters appears only with the pose it checked; on other poses a note links to that pose.
  • Legend: C ligand and C protein; each interaction type counts residues, as in the Contacts list (atom-level contacts in its tooltip). Picking a residue no longer recolours it.
  • Pocket residues in sequence order; the number of surface atoms per pocket from P2Rank; labels stay readable at the edge of the view.
  • The GitHub link points to BIMSBbioinfo/PocketVina.

· Preview build

  • New name: PocketVina Atlas. New design: one font family, white background, plain tables.
  • Every number on the site now comes from meta.json, with its definition and source; see About, Numbers.
  • The pose index is split: the offsets of the highest-affinity poses load with a pair, the offsets of all modes only when modes are shown.
  • Large JSON files are also published gzip-compressed and unpacked in the browser.
  • PV identifiers: every protein, ligand, pair, pose and pocket has one, shown with a Copy button. Drug pages live at their ligand ID; ChEMBL IDs and drug names redirect there.
  • Random pair: a random protein and a random docked drug, with a fit rule; Random protein and Random drug links on the overview.
  • Indications from ChEMBL on drug pages, and a known-target line in the pair panel (preview: ten drugs).
  • The protein page opens on the structure again: viewer and tabs (Top hits, Selected pair, Pockets, Download), with Annotations folded under the title.
  • The viewer colours the pose by element, draws the interactions Mol* finds and labels the residues near the pose; a legend explains the colours.
  • Pockets list their residues; a residue opens in 3D. A pair shows its contacts and its highest affinity in each pocket.
  • Theme icons, link icons, a footer in columns, Spin a random pair, and a guide with screenshots.

· Preview build

  • First public preview with mock data: search over all proteins and compounds, full docking data for three proteins.