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

ChemLink v2.0.0 — Open source, peptide docking and CPU docking Latest
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@MatizS27 MatizS27 released this 26 Oct 17:37
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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ChemLink v1.0.0 — Initial stable release

ChemLink v1.0.0 — Initial stable release

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@PipeJF9 PipeJF9 released this 22 May 23:37
v1.0.0
51c9dd9

ChemLink v1.0.0

First stable release of ChemLink, a modular orchestration platform for computational chemistry on HPC clusters.

Features

  • Docking pipeline — end-to-end automation: active site detection (fpocket), receptor/ligand preparation (MGLTools + AutoGrid4), GPU-accelerated docking (AutoDock-GPU), and results analysis
  • Molecular dynamics pipeline — full GROMACS 2025.4 workflow supporting six biological system types from topology preparation to trajectory analysis
  • Single-node mode — parallel ligand processing with configurable worker count (up to 24 workers tested)
  • Multi-node mode — distributed docking via SLURM Job Arrays across GPU nodes
  • Unified CLI — chemlink docking and chemlink dynamics commands with chemlink doctor for environment verification
  • Reproducibility — timestamped run directories, stats.json per campaign, versioned Conda environments (bio, mgl_legacy)
  • Monitoring — Prometheus + Grafana integration for real-time resource tracking
  • Docker support — containerized execution for isolated environments
  • Test dataset — ready-to-run inputs: receptors (1HSG, 6LU7, 3PTB from RCSB PDB) and ligands (Indinavir, Nirmatrelvir, Benzamidine, Ibuprofen, Aspirin, Caffeine from PubChem)

Validated performance (1 000 ligands)

Mode Duration Throughput
Single-node Opt (24 workers) 54 min 18.5 lig/min
Single-node Min (1 worker) 335 min 3.0 lig/min
Multi-node (3 GPUs, SLURM) 31.6 min 31.6 lig/min

Speedup vs single-node: up to 2.2× with 3 GPUs.

Installation

# Base installation (Python layer + Conda environments)
curl -fsSL https://raw.githubusercontent.com/PipeJF9/chemlink/main/install.sh | bash

# Full installation (includes fpocket, AutoGrid4, AutoDock-GPU, GROMACS 2025.4)
curl -fsSL https://raw.githubusercontent.com/PipeJF9/chemlink/main/install.sh | bash -s -- --full

Quick test

chemlink doctor
chemlink docking --receptor data/test/receptors/1hsg.pdb --ligands data/test/ligands/indinavir.sdf --output data/output/test
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