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v2.0.0

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@rvhonorato rvhonorato released this 04 Mar 13:24
41f964c

gdock v2.0.0 🐙

This release marks a complete rewrite of gdock in Rust 🦀, replacing the previous Python implementation.

The core algorithm, scoring function, and clustering are all implemented natively with no runtime dependencies🎉

What's new since v1:

  • Rust rewrite: The code has been completely re-written in Rust, the scoring function is now native and all calculations are done by gdock itself (previously it was done by dcomplex). With this re-write we achieve very low run times of ~15s per docking run on standard hardware.
  • New CLI: We now have three subcommands: run (full docking), score (energy evaluation only), restraints (generate restraints from a native structure)
  • Calibrated scoring weights and validated success rates: VDW, electrostatics, and desolvation weights optimized against the Dockground decoy set, and benchmarked using the protein-protein docking benchmark v5; 95.9% success rate (260/271 complexes with at least one acceptable model, DockQ ≥ 0.23) - more info on gdock-benchmark
  • Native FCC clustering: reimplemented the frequency of common contacts algorithm in Rust, no external tools needed
  • Library crate: gdock can also be used as a Rust library, with WebAssembly bindings powering https://gdock.org - more on gdock-wasm
  • Pre-built binaries: available for Linux (x86_64, aarch64, musl) and macOS (x86_64, aarch64, universal)