NeonCortex
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Software for ligand-protein interaction?
Hi! I've been lurking this board for a few years, but never been an active member. I've been getting more into computational chemistry lately. Mostly
I've been using software for molecular visualizations and to better understand spectrographic data such as NMR, but since I've become very interested
in biochemistry and Q/SAR the use of computers are getting more and more interesting.
I've recently installed a new system, and have ChemOffice, ChemSketch and PyMOL on it. I have the PC-GAMESS for Windows package, but haven't installed
it yet. Hopefully I can integrate it with Chem3D. Chem3D seems to be a pretty competent program, but as usual when it comes to this kind of programs
it requires a fair bit of studying to use it properly.
What I really would like to do is to be able to do ligand-receptor interaction studies in silico. I realize this is a complicated task for any program
at the present time, but I know there is software for it. My goal is to take known ligands and in vitro/vivo data on them, and then modify the
structure to predict how the binding will change. The goal is to identify pharmacophore models, how to enhance binding properties and to be able to
suggest alternative molecules with similar activity.
What I'm also looking for is software for chemical analysis simulation (NMR, MS, IR, cromatography, X-RAY). A program for analysis of diffraction
patterns, more intuitive than WinGX, would be much appreciated.
Any suggestions on quality software I should consider, and links to them if available, would be much appreciated. Software for Windows is preferred.
Open source and freeware is great, especially since my use is non-commercial and funds are very scarse, but I'd rather have one program that can
perform most of the tasks.
Finally, I would like to recommend PyMOL for protein visualization. It's free for non-commercial use, and can be used to generate models straight from
pdb-files.
http://www.delanoscientific.com/
Lighting up your cortex since birth
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Polverone
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I believe that you want "docking" software. I was going to tell you that I don't know of any well-established, free docking software, but it seems
that as of version 4 the well-known AutoDock is freely available under the GPL. Most docking programs, including AutoDock, appear to rely on gas phase force field models (perhaps
combined with additional scoring functions), which are efficient but not the best approximation to conditions in vivo or even in vitro. Some docking
software permits the use of semi-empirical, ab initio, or DFT approaches to quantum chemistry, sometimes with implicit solvation too, but I haven't
stumbled across free software that permits that. The computational demands of those approaches is also much higher than that of force field models.
If you do find some free docking software that permits the use of quantum chemistry, it can be used for secondary screening after you've identified a
promising candidate pool from force field models. Something that allows use of PC-GAMESS for the quantum calculations would be ideal, since it's the
fastest free quantum chemistry software I know of. At best this will weed out false positives. It won't help if the force field deficiencies lead to
underrated ligand affinities.
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NeonCortex
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Thank you very much! Downloaded it and looking forward to try it!
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longimanus
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I would strongly suggest the UCSF program package DOCK 6. One will need a lot of time to customise the package, it's deffinately not graphical or user-friendly. However, the AMBER score gave some
nice corelations with receptor affinity for me.
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NeonCortex
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I now have Autodock and ArgusLab. Will probably get dock 6, but maybe save that until I'm more at ease with the methodology and other programs first.
I thank you for your help, and will report any interesting progress I make.
I must also say I was positively surprised by the fact that there were several entirely free docking packages out there that seems pretty competent.
[Edited on 07-10-26 by NeonCortex]
[Edited on 07-10-26 by NeonCortex]
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