Jump to source code and data related to publications or classes, or recommended software.
We have contributed source code and data to repositories on GitHub and SimTK.
Occupancy Fingerprinter is our fast code to compute occupany fingerprints, a grid of points that are one when the space near them contains and atom and zero otherwise. It is described in Journal of Chemical Information and Modeling, acs.jcim.3c01518 (2024). We originally described occupancy fingerprints in Journal of Chemical Information and Modeling 58, 1915–1925 (2018).
JAX AMBER is our implementation of the AMBER force field in JAX, a numerical framework used in machine learning. We used the code in Journal of Chemical Physics 159, 124104 (2023).
pdb2amber which prepares membrane protein systems for simulation with the AMBER force field.
Robosample, which uses algorithms from robotics to perform molecular dynamics simulations.
AlGDock is our main code to estimate the binding potential of mean force, the binding free energy between a flexible small molecules and a rigid protein. This is a key part of estimating the standard binding free energy using implicit ligand theory. It is described in Journal of Computational Chemistry 41, 715–730 (2020).
A symmetric estimator for nonequilibrium path-ensemble averages, as described in Journal of Chemical Physics 151, 194103 (2019).
BPMFwFFT is a code to estimate the binding PMF based on the Fast Fourier transform. It is described in Journal of Computational Chemistry 39, 621–636 (2018).
bitc is code from John Chodera’s group for the Bayesian analysis of isothermal titration calorimetry experiments, as described in PloS One 13, e0203224 (2018).
An estimator for relative binding free energy calculations based on implicit ligand theory, as described in Journal of Chemical Physics 148, 104114 (2018).
An estimator for absolute binding free energy calculations based on implicit ligand theory, as described in Journal of Chemical Physics 137, 104106 (2012).
MATLAB code for analyzing biased experiments, as described in Journal of Physical Chemistry B 111, 4137–4140 (2007) and Physical Review E 74, 61120 (2006).
David has taught an advanced undergraduate class on computational chemistry and drug design and made resources including lecture notes and website code available.
David has also worked with interprofessional project (IPRO) groups at Illinois Tech to develop a web-based graphical user interface for AlGDock. An IPRO team has also developed image analysis for ball-and-stick models to generate chemical graphs, which may be used for interactive exercises in organic chemistry.
Anaconda Python - the Python programming language is widely used in the scientific community. It includes many packages for data analysis and visualization. Anaconda provides a high-quality management of virtual environments.
Zotero - It can be difficult to keep track of the scientific papers that you’ve read and would like to cite in your own articles. Zotero is a free reference manager that will organize files for you and generate bibliographies. It interfaces with word processors like Microsoft Word and Google Drive, among others.
Visual Molecular Dynamics (VMD) - molecular visualization code, specialized for molecular dynamics trajectories. The “Using VMD” tutorial is a good starting point.
Not Another Molecular Dynamics (NAMD) - molecular dynamics code, with nice documentation and tutorials. Most relevant to the group are the molecular dynamics tutorial, and the tutorials on protein:ligand standard binding free energies and alchemical free energy perturbation.
