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ChemLink v2.0.0 — Open source, peptide docking and CPU docking

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@MatizS27 MatizS27 released this 26 Oct 17:37
· 11 commits to main since this release
v2.0.0
c835374

ChemLink v2.0.0

ChemLink is now open source under AGPL-3.0, with a commercial license available from Athalea. The website and documentation have moved to athalea.co/chemlink.

⚠️ Breaking changes

  • License: ChemLink is relicensed as AGPL-3.0 + commercial. See LICENSING.md and THIRD_PARTY_LICENSES.md.
  • CLI: inputs are now standardised across pipelines (-ir/--input-receptors, -il/--input-ligands, -ic/--input-cofactor, -ip/--input-peptides, -o/--output). The v1.0.0 flags --ligands, --ligand-dir, --receptor-dir, --protein, --workers, --max-workers, --mode and the tool-path flags were removed. Worker counts are now set per stage (-r, -l, -a, -d).
  • Commands: chemlink dynamics is now chemlink dynamic. Docking is split into prepare, full, flow, receptor, ligand, active-site, run and analyze subcommands.
  • Repository: moved to athalea-software/chemlink. The installer and docs use the new URLs.

New

  • Peptide–protein docking: chemlink docking peptide, using LightDock with PRODIGY affinity cross-checks and a robustness pipeline (robust lightdock | audit | prodigy | combine | all).
  • CPU docking with AutoDock Vina. The default --engine both runs GPU and CPU docking together.
  • Flexible-receptor docking, automatic co-crystal centre detection, redocking and receptors with structural or functional cofactors (--keep-cofactors).
  • Docking ranking: robust z-score is now the main combined ranking signal.
  • Molecular dynamics:
    • protein–ligand + cofactor systems
    • choice of force field and water model for protein and peptide systems
    • 2 replicas per protein–ligand simulation by default
    • resume and analyze subcommands
  • Binding energy: MM-PBSA / MM-GBSA through gmx_MMPBSA, with an entropy term (--mmpbsa-entropy) and its own settings for method, cores, frames and salt.
  • CLI and TUI:
    • a new terminal design system
    • an interactive TUI
    • chemlink demo (preview without tools or a GPU)
    • chemlink update
    • chemlink completion
    • --no-color / --plain output
  • Output, docs and README are now in English.

Fixes and robustness

  • Ligand validation before docking and MD, with Open Babel 3.2.1 bond-order perception and hydrogen stripping for over-valent nitrogens.
  • Better automatic charge detection.
  • Fixes for the handling of non-canonical residues, PDBQT glue atoms and pose element export.
  • Transient preparation crashes are now retried.
  • Cleaner logs and warnings across the docking and MD workflows.
  • Installer fixes: real requirements and csh added to the Docker image.

Removed

  • The FEP prototype and committed run outputs.

Full changelog: v1.0.0...v2.0.0

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