Scientific Software from the Gilson Lab
Provided as-is with absolutely no warranty of safety or fitness for any particular purpose!
 


Second Generation Mining Minima Software (M2)
zip compression, 31MB
This is version 2.A.2, August, 2009, the first full release of our software for computing host-guest binding affinities1,2. The distribution includes source code, Windows and Linux executables and makefiles, sample input and output files, scripts for automation on Linux, a Windows GUI, and a detailed user manual. Some subroutines are provided for redistribution by courtesy of other groups. If you publish work based on the M2 software or any of its modules, please cite accordingly. The main M2 citations are:







ACCENT Mutual Information Expansion Code
This is version 1.2 (July, 2009) of our software which uses a histogram-based implementation of the mutual information expansion to extract extracting configurational entropy from dynamics or Monte Carlo simulation data3. In this version, all of the Python code from the prior versions has been removed, leaving only FORTRAN90. This change avoids some of the installation and Python version issues of prior ACCENT versions. Also, the input options provide more detailed control of the entropy calculations. The distribution provide source code and includes a user-manual, an illustrative example, and a standalone code to convert the ASCII bond-angle-torsion files from AMBER2ACCENT (below) to binary for processing by ACCENT. This distribution is completely free, though we ask for your name and email address to help us with software-support and with grant reporting. If you publish work based on this method, please cite:


AMBER2ACCENT
A PERL script that uses the program ptraj to extract the bond-lengths, bond-angles and torsion angles from MD snapshots generated with the simulation program AMBER , so that they can be processed with the ACCENT entropy code (above). This script was created by Dr. Thomas Steinbrecher (steinbrt@scripps.edu) and is posted here for free distribution with his kind permission. It is also available here.




Molecular coordinate system tools
A discussion of molecular coordinate systems and and a MATLAB script to convert Bond-Angle-Torsion coordinates to Anchored Cartesians4. Kindly provided by Sandeep Somani.





HYBRID Titration Code
This software implements a hybrid exhaustive/mean-field approach to solving the multiple-site titration problem in proteins5. This completely free distribution includes source code, precompiled executables for Windows, Linux and Irix (remember Irix?), a simple user-manual, and sample input and output files. If you use this method, please cite:





Substrate Envelope Software
This open-source (GPL) software allows calculation and use of the substrate envelope hypothesis to help design enzyme inhibitors to evade resistance mutations6. The software was written by Visvaldas Kairys, in collaboration with Viney Lather, Celia Schiffer, Mike Gilson, and Miguel Fernandes. (The download link goes to the Fernandes lab's web-site.) The download includes a README file, three Fortran codes, and sample files. If you use this method, please cite:


References
  1. Chen,W., Chang,C. and Gilson,M.K. Calculation of cyclodextrin binding affinities: Energy, entropy and implications for drug design. Biophys. J., 87:3035-3049, 2004.
  2. Chang,C. and Gilson,M.K. Free energy, entropy, and induced fit in host-guest recognition. J.Am.Chem.Soc. 126:13156-13164, 2004.
  3. Killian,B.J., Kravitz,J.Y., Gilson,M.K., Extraction of configurational entropy from molecular simulations via an expansion approximation, J. Chem. Phys. 127:024107, 2007.
  4. Somani S, Killian BJ and Gilson MK, Sampling conformations in high dimensions using low dimensional distribution functions. Journal of Chemical Physics, 130, 134102,2009
  5. Gilson,M.K., Multiple-site titration and molecular modelling: Two rapid methods for computing energies and forces for ionizable groups in proteins, Proteins 15:266-282, 1993.
  6. Kairys,V, Gilson,MK, Lather,V, Schiffer,CA, and Fernandes,MX. Chem. Biol. Drug Des. 2009, v. 74, p.234-45.