Open source

Code

We actively maintain and share all our tools. Everything we build is open source: free to use, study, and contribute to.

Open-source software

Our tools

AutoDock Vina

ccsb-scripps/AutoDock-Vina

AutoDock Vina is one of the fastest and most widely used open-source docking engines. It is a turnkey program based on a simple scoring function and rapid gradient-optimization conformational search. Originally designed by Dr. Oleg Trott, it is now maintained and developed by the Forli Lab. Up to 100x faster than AutoDock 4, with support for flexible docking, macrocycles, explicit water molecules, and Python bindings introduced in v1.2.

Computing Vina grid ... done.
Performing docking (random seed: -909708777) ...
  0%   10   20   30   40   50   60   70   80   90   100%
  |----|----|----|----|----|----|----|----|----|----| 
  ***************************************************

  mode |   affinity | dist from best mode
       | (kcal/mol) | rmsd l.b.| rmsd u.b.
  -----+------------+----------+----------
     1       -13.35          0          0
     2       -11.69      3.967      12.04
     3       -10.53      3.353      12.33
     4       -10.38      1.452      2.078
     5       -9.745      2.515      12.73
     6       -9.417      1.709      13.35
     7       -9.155      3.991      12.32
     8       -9.117      3.956      12.11
     9       -9.051       2.15      4.833
CPU times: user 1.37 s, sys: 221 ms, total: 1.59 s

AutoDock GPU

ccsb-scripps/AutoDock-GPU

AutoDock for GPUs and other accelerators. Dramatically faster virtual screening for large compound libraries.

Meeko

forlilab/Meeko

Interfacing RDKit and AutoDock to prepare small molecules for docking. Handles parametrization and software interoperability.

Ringtail

forlilab/Ringtail

Storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina. Handles large-scale docking results efficiently.

Scrubber

forlilab/molscrub

Process large numbers of small molecules for docking with AutoDock. Handles enumeration, filtering, and preparation at scale.

Waterkit

forlilab/waterkit

Predicts water molecule placement and energy in ligand binding sites, improving docking accuracy for hydrated binding pockets.

Cosolvkit

forlilab/cosolvkit

Tool for cosolvent MD preparation and analysis, enabling mixed-solvent molecular dynamics simulations for binding site characterization.

Online services

Web tools

Böttcher Score Calculator

Calculate molecular complexity as defined by Thomas Böttcher. An online tool for medicinal chemists to assess compound complexity directly in the browser.