Pinned Repositories
Allostery-Analysis
Use to generate covariance, hENM Hessian and allosteric paths
CHEM571A_2019
Class notes, homework assignments and information for CHEM 571A Quantum Chemistry
CHEM573F
drugBind
Machine learning python code for predicting binding affinity
force-match
Python script for calculating force potentials in MD simulations
GMM-Positions
Gaussian Mixture Model for particle positions using alignments
ISSPA-Force-Cuda
Liquid-Argon-Monte-Carlo
pLDA
shapeGMMTorch
mccullaghlab's Repositories
mccullaghlab/force-match
Python script for calculating force potentials in MD simulations
mccullaghlab/drugBind
Machine learning python code for predicting binding affinity
mccullaghlab/Liquid-Argon-Monte-Carlo
mccullaghlab/RGYR
Python code, using MDAnalysis, to calculate the radius of gyration of a solute in a MD trajectory.
mccullaghlab/2D-Ising-Exam
mccullaghlab/Align-pdb-with-atom-selection
A script two align two pdbs given an atom selection. The overall number of atoms in the pdbs need not be the same. The atom selections must contain the same number of atoms however.
mccullaghlab/chain_growth
mccullaghlab/chain_growth_program
chain growth into a sphere using minimum energy addition criteria
mccullaghlab/Coarse-grained-Charge-Fitting
Code used for paper
mccullaghlab/dbdock
Using machine learning to predict the binding affinity of new drug molecules to proteins
mccullaghlab/DCD_Writer
Python code, using MDAnalysis, to take in a .dcd file and write a new .dcd file. Useful for turncating large .dcd files down to smaller file sizes by removing solvent/unwanted atoms.
mccullaghlab/DENV-NS3h
Repository for all scripts used in the DENV-NS3h paper.
mccullaghlab/drug-bind-docking
mccullaghlab/esp_grid
mccullaghlab/fit_to_linear
given a set of data this code computes the probability distribution, free energy and then fits that free energy to a parabola. It spits out the force constant for the fit parabola.
mccullaghlab/Fixman-Theory-Coding-Day-1
mccullaghlab/fixman_day5_class_files
mccullaghlab/force-match-wgrouping
mccullaghlab/gromacs_pair_energies
Script to compute pair energies between four groups of atoms. It also prints the center-of-mass distance between groups 1 and 2. Pair energy consists of LJ and coulomb.
mccullaghlab/helical-parameters
python script to compute helical parameters for planar structures
mccullaghlab/install_rdkit.sh
Shell script for installing rdkit over an Anaconda Python 2.7 distribution
mccullaghlab/Integrate-Extract-Lambda
Extract lambda data from NAMD log files and integrate.
mccullaghlab/IS-SPA
Code to run an IS-SPA simulation
mccullaghlab/Iterative-Boltzmann
mccullaghlab/rmsd_by_selection
Compute the RMSD for a given selection. Currently only works for nucleic acids. One version computes RMSD using MDAnalysis routine one by hand.
mccullaghlab/ss_helical_pca
Compute the prinicpal components of the distance and angle helical parameters
mccullaghlab/US-pdbs-from-trajectory
Grab pdbs from a tajectory for starting structures for US
mccullaghlab/us_amber