I docked many ligands into one protein and would like to make a pharmacophore representation of the better docking results.
Is there any free software that allow me to use the docking results as they are, instead of realigning them from scratch?
Dear Paolo,
You may use PharmDock:
This program is free and you can read the publication on this software using the following link:
https://jcheminf.springeropen.com/articles/10.1186/1758-2946-6-14
A protein pharmacophore-based docking program, PharmDock, has been made available with a PyMOL plugin. PharmDock and the PyMOL plugin are freely available from http://people.pharmacy.purdue.edu/~mlill/software/pharmdock.
PharmDock: a pharmacophore-based docking program
Bingjie Hu and
Markus A LillEmail author
Journal of Cheminformatics20146:14
DOI: 10.1186/1758-2946-6-14
Published: 16 April 2014
Abstract
Background
Protein-based pharmacophore models are enriched with the information of potential interactions between ligands and the protein target. We have shown in a previous study that protein-based pharmacophore models can be applied for ligand pose prediction and pose ranking. In this publication, we present a new pharmacophore-based docking program PharmDock that combines pose sampling and ranking based on optimized protein-based pharmacophore models with local optimization using an empirical scoring function.
Results
Tests of PharmDock on ligand pose prediction, binding affinity estimation, compound ranking and virtual screening yielded comparable or better performance to existing and widely used docking programs. The docking program comes with an easy-to-use GUI within PyMOL. Two features have been incorporated in the program suite that allow for user-defined guidance of the docking process based on previous experimental data. Docking with those features demonstrated superior performance compared to unbiased docking.
Conclusion
A protein pharmacophore-based docking program, PharmDock, has been made available with a PyMOL plugin. PharmDock and the PyMOL plugin are freely available fromhttp://people.pharmacy.purdue.edu/~mlill/software/pharmdock.
Keywords
Protein pharmacophores Docking Scoring Biased docking Constraint docking Confined docking GUI PyMOL
Hoping this will be helpful,
Rafik
Thank you very much for the suggestion. PharmDock seems to be very useful.
Do you know if I can import my docking results obtained with other software or if I have to use PharmDock for docking and then make the pharmacophore representation?
Dear Paolo,
I believe that you can import results from the following programs to be used in PharmDock:
Surflex, GOLD, Glide SP, AutoDock, LigandFit and FlexX
Rafik
That would be perfect.
I'll absolutely give it a try. Thank you very much again.
Dear Gaokeng,
thank you for the suggestion. I agree with you with ligandscout, but as far as I know, it is not a free software. I know one can obtain a free trial period of one month, but this is not what I'm searching for. Do you know of similar software that are available free of charge?
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