Docking

=Docking Experiments= Docking runs against various targets can be found here

= = =Open Source Software Used in Docking Work Flow= =Pocket Detection=

fpocket
link

SPPIDER
link =Conformer Generation=

Frog2
link - see also this list =Docking Programs=

AutoDoc Vina
link PyRX (gui that uses vina, open babel, etc)

FRED
link

THINK
Docking Descriptions and Experiments [| link]

Arguslab
[|link]

Quantum
[|link]

OOPSE (from Open Source Science Project)
[|link] =Molecular Minimization=

Open Babel
code [single molecule] obabel whatever.smi --gen3d -O whatever.sdf [batch] obabel smiles.smi --gen3d -O ligand*.pdb code

MOPAC
[|Open Source Version 7]

Marvin
code [convert single molecule from SMILES to pdb] molconvert -3 pdb taxol.smi -o taxol.pdb code =SubStructure Searching=

OpenBabel
[|tutorial]

Marvin
media type="custom" key="7675"