hmacdope
Senior Software Scientist @asapdiscovery @choderalab
ASAP Discovery / @omsfMemorial Sloan Kettering Cancer Center
Pinned Repositories
asapdiscovery
Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium
alchemiscale
protein-ligand alchemical free energy calculations via Folding@Home
distopia
trying out SSE instructions for faster distance calculations
hmacdope.github.io
mda-benchbot
Benchmarking bot for MDAnalysis
MDA-core-playground
Playground for developing Cythonized core datastructures for MDAnalysis
mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
MDAnalysis.github.io
MDAnalysis home page mdanalysis.org as GitHub pages.
minimal_molview
Render PDB files to viewable HTML with 3DMol
pytng
Python bindings for TNG file format
hmacdope's Repositories
hmacdope/AI-ML-Applications-on-Gadi_Parallel-Python
hmacdope/nci-xarray-course
Course for learning xarray
hmacdope/nci-dask-course
hmacdope/NiAlN_EDIP_Fitting_DFT
hmacdope/NCI_NumPy_intro
hmacdope/Distance_array_wrapper
hmacdope/git-novice
Version Control with Git
hmacdope/sql-ecology-lesson
Data Management with SQL for Ecologists
hmacdope/MDA-core-playground
Playground for developing Cythonized core datastructures for MDAnalysis
hmacdope/PsaBC_dynamics
Investigating the dynamics of the PsaBC ABC importer
hmacdope/PsaA_metal_ion_FF_comparison
Supplementary data for paper on PsaA force-field comparison.
hmacdope/mda-benchbot
Benchmarking bot for MDAnalysis
hmacdope/epithelial_membrane
Supplementary data files for "A Computational Model Replicating the Lipid Composition of a Human Epithelial Plasma Membrane "
hmacdope/TmEnc_Flux
MD trajectories and analysis scripts for a forthcoming paper.
hmacdope/Neuronal_PM_complexity_MARTINI
hmacdope/Abaumanii_MARTINI_membrane
hmacdope/Fatty-Acid-Aryl-Urea-QC-data
SI for fatty acid aryl urea paper
hmacdope/python-novice-gapminder
Plotting and Programming in Python
hmacdope/lipyds
hmacdope/sushi
Computer set-ups, shell environments, installation notes, etc.
hmacdope/Carbamide_uncouplers
Supplementary data
hmacdope/StoR_accuracy_comparison
Basic program to investigate accuracy of fractional to real space conversion code from MDAnalysis
hmacdope/trapezoidal.rs
Fun little toy program to integrate functions using trapezoidal rule in rust
hmacdope/UserGuide
User Guide for MDAnalysis (GSoD Project)
hmacdope/Rh_Carbido_NMR
hmacdope/Rh_NHCs_NMR
Calculating chemical shifts of Rhodium containing analogues of N-heterocyclic carbenes
hmacdope/PBC_N_OF_BONDS
Periodic boundary respecting N_OF_BONDS collective variable for use with the AMBER NFE free energy code
hmacdope/IQmol
IQmol is an open source molecular editor and visualization package
hmacdope/cmake-modules
Additional CMake functionality. Most of the modules are from Ryan Pavlik (https://github.com/rpavlik/cmake-modules)
hmacdope/plumed2
Development version of plumed 2