Software originally introduced in the paper:
Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV-1 protease and F-ATP synthaseSindhikara, D. J., Yoshida, N. and Hirata, F. (2012), Placevent:
An algorithm for prediction of explicit solvent atom
distribution—Application to HIV-1 protease and F-ATP synthase. J.
Comput. Chem.. doi: 10.1002/jcc.22984
This paper is available at Journal of Computational Chemistry
(link)
contact
Abstract:
We have created an
algorithm for automatically predicting the explicit solvent atom distribution
of biomolecules using 3D-RISM. This procedure predicts optimal location of
solvent molecules and ions given a rigid biomolecular structure and the solvent
composition. Our results give excellent agreement with experimental structure
with an average prediction error of 0.45-0.65 Å. Our method can be performed
directly on 3D-RISM output within minutes.
Superposition of 3D-RISM and placed waters in HIV-1 Protease
Video: Inside HIV-1 Protease:
Glassy green: 3D-RISM water oxygen isosurface
Spheres: "Placed" water oxygens, color denotes g(r) from high (blue) to medium (white) to low (red).
Software information:
The current version (Feb 9, 2012) can be downloaded here. Please let me know if you have any problems.
The software was written in python 2.7 utilizing the SciPy package. For quick installation of SciPy I recommend using the Enthought scientific python distribution (free for academics).
The program operates on .dx files which are the default from AMBER
output. If you use a 3DRISM in GAMESS, please try my unofficial
conversion software somewhere on this page.
Tutorial:
I have written a quick tutorial for using the software using AMBERtools! Please give it a try! |
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ď Daniel Sindhikara, Feb 9, 2012 4:57 AM
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http://goo.gl/uLohs