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Docking

Protein-protein docking

Datasets

  • Dockground — Benchmarks, decoys, templates, and other knowledge resources for docking.
  • PDBbind ‒ Experimentally measured binding affinities for biomolecular complexes in the PDB.

Software

  • DOT — FFT-based rigid body docking, with an additive correlation term to consider electrostatics. [BSD-3-Clause]
  • FTDock — FFT-based rigid body docking, with an additive correlation term to consider electrostatics. [GPL-v2]
  • HADDOCK — Different from most other tools in that it uses CNS, optimizes the protein backbone, and allows the incorporation of experimental restraints. Flexible refinement using CNS with ambiguous interaction restraints (AIRs). [Proprietary]
  • HDOCK — FFT-based rigid body docking, with additive correlation terms and template-based scoring. One of the top servers in recent CAPRI experiments. The HDOCKlite standalone package is also available. [📖, Proprietary]
  • HEX — Uses a spherical polar Fourier (SPF) protein docking algorithm. 1D (SPF) sampling is very marginally less successful than 3D sampling, but is much faster, especially on a GPU. [📖, 📖, GPU, Proprietary]
  • LightDock — LightDock is a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm. The LightDock framework is highly versatile, with many options that can be further developed and optimized by the users: it can accept any user-defined scoring function, can use local gradient-free minimization, the simulation can be restrained from the beginning to focus on user-assigned interacting regions, it supports residue restraints in both receptor and ligand partners. Although not explicitly stated, it is probably slower than FFT-based methods? [GPLv3]
  • MEGADOCK — An ultra-high-performance protein-protein docking for heterogeneous supercomputers. [📖, GPU, Apache-2 ???].
  • PIPER — FFT-based rigid body docking, with additive correlation terms. Used by the ClusPro web server, which is one of the best-performing web servers in recent CAPRI experiments. Not available for download? [📖, Proprietary]
  • pyDock — Used FTDock to generate complexes and scores those complexes using a custom function. [Proprietary]
  • ZDOCK ★ — FFT-based rigid body docking, with additive correlation terms to consider electrostatics and salivation. [Proprietary]

References

Protein-small molecule docking

Software

  • AutoDock Vina — MC based docking software. Free for academic usage. Flexible ligand. Flexible protein side chains. Maintained by the Molecular Graphics Laboratory, The Scripps Research Institute, la Jolla. [Apache-2]
  • GNINA — gnina (pronounced NEE-na) is a molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks. It is a fork of smina, which is a fork of AutoDock Vina. [YouTube 🎥, Apache-2]
  • iDock — idock is a standalone tool for structure-based virtual screening powered by fast and flexible ligand docking. Fork of AutoDock Vina. [Apache-2]
  • smina — A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project. [Apache-2]

References