Directory of in silico Drug Design tools - FAQ
More information can be found on Click2Drug, which provides a comprehensive list of computer-aided drug design
software and web services, both for structure-based and ligand-based calculations.
This article is translated to Serbo-Croatian
language by Jovana Milutinovich.
I need to draw rapidly the chemical structure of a compound.
Several web services are available for that, like ChemWriter
, the Marvin molecule editor and viewer
and the Molinspiration WebME Molecule Editor
I have the SMILES of a molecule and would like to know to which molecule it corresponds, or get a drawing of it.
You can use the Smi2Depict
web service to do draw the chemical structure of your molecule from a SMILES. You can also see it in 3D using the Corina online demo
I have a molecule file in one format, but would like to convert it into another format.
You can use the E-Babel
I would like to generate several possible conformers of my molecule.
You can use Frog2
I have a small molecule, and would like to know to which protein it might bind.
web service tries to answer this question using reverse docking. The PharmMapper
service does it using a pharmacophore mapping approach.
I have a small molecule, and would like to find similar ones.
This can be done using the Superimposé
Is it possible to predict the binding sites on my protein?
This can be done online using the 3DLigandSite
I would like to dock a molecule into a protein binding site.
Several web services are available for that like SwissDock
, which are free for academic users, and DockingServer
, which is free for academic users for a limited number of dockings per day.
I have a protein, and would like to perform an extensive virtual screening of small molecules on it.
This can be done using the Blaster
I need to perform some structure-based calculations, but there is no experimental structure for my protein. How can I obtain a structural model of my protein?
The homology model of your protein might have been already calculated and may be available in the SWISS-MODEL Repository
or at ModBase
. Otherwise, you can calculate the homology model using the SWISS-MODEL
I need to perform Molecular Mechanics calculations on a protein-ligand complex, but I don't have parameters for the small molecule.
You can use the SwissParam
web service to get parameters and topologies for small organic molecules, for use with CHARMM and GROMACS. Dundee PRODRG2 Server
also provides topology and parameters for GROMACS.
I need to perform Molecular Mechanics calculations on a protein, but don't know how to setup the system.
You can use the CHARMMing.org
web service to setup a protein for use with CHARMM
How can I estimate the affinity of a small molecule for a protein?
Several web services are available, like DrugScoreONLINE
, and the BAPPL server
or BAPPL-Z server
. The latter can be used for Zinc-based proteins.
How can I design a ligand of a protein, based on the 3D structure of the binding site?
Scaffold-hopping can be performed online using the e-LEA3D
I would like to calculate physico-chemical parameters and descriptors of several small molecules to perform QSAR calculations.
This can be performed using the MolInfo
How can I estimate the logP value of my molecule?
the web service ALOGPS
estimates logP values using several different approaches. Other web services are alos available, like XScore-LogP
Can I estimate the toxicity of a small molecule?
You can do this using VirtualToxLab
, the OSIRIS Property Explorer
Can I estimate ADME parameters of a small molecule?
You can do this using ALOGPS
, the OSIRIS Property Explorer
, the MODEL - Molecular Descriptor Lab
and the Free ADME Tools