Computer Aided Drug Design (CAAD) Programs

• AutoGrow4: AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. AutoGrow4 is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands.
      Documentation, Forum, & Download: https://durrantlab.pitt.edu/autogrow4/
      Git Repository: https://git.durrantlab.pitt.edu/jdurrant/autogrow4.git
  

Cheminformatic Programs

• Gypsum-DL: Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.
      Documentation, Forum, & Download: https://durrantlab.pitt.edu/gypsum-dl/
      Git Repository: https://git.durrantlab.pitt.edu/jdurrant/gypsum_dl.git

• SMILESMerge: SMILESMerge is a free, open-source program that merges two SMILES strings to produce a novel child compound. SMILESMerge uses the AutoGrow4 crossover algorithm to create de novo compounds and was inspired by the program LigMerge. SMILESMerge also provides the option to automate 1/2D SMILES to 3D conversion using Gypsum-DL as well as ADME-PK filters using GlauconiteFilter.
      Git Repository: https://github.com/Jacob-Spiegel/SMILESMerge.git
      
  

• SMILESClickChem: SMILESClickChem is a free, open-source program that creates novel compounds by performing in silico reactions. SMILESClickChem uses the AutoGrow4 mutation algorithm to create de novo compounds and was inspired by the program AutoClickChem. SMILESClickChem provides a predefined library of 94 high-yielding chemical reactions, however, its intuitive plugin-style architecture allows for the easy expansion of reaction sets and libraries of reactants. SMILESClickChem also provides the option to automate 1/2D SMILES to 3D conversion using Gypsum-DL as well as ADME-PK filters using GlauconiteFilter.
      Git Repository: https://github.com/Jacob-Spiegel/SMILESClickChem.git
      
  

• GlauconiteFilter: GlauconiteFilter is a free, open-source program for parallelized ADME-PK chemical filtration. GlauconiteFilter uses the AutoGrow4 filtration algorithm to SMILES strings. It is a highly parallelized algorithm that has been test on both SMP and MPI high performance computing environments. GlauconiteFilter provides nine predefined chemical filters, however, its intuitive plugin-style architecture allows for the easy expansion of filter options. GlauconiteFilter also provides the option to automate 1/2D SMILES to 3D conversion using Gypsum-DL.
      Git Repository: https://github.com/Jacob-Spiegel/GlauconiteFilter.git