Programming
Python, Bash, AWK, MATLAB, R, Mathematica, LaTeX
Molecular Simulation
AMBER, MOE, CHARMM, NAMD, OpenMM, GROMACS, WESTPA, BrownDye, VMD, MDTraj, MDAnalysis, PyMOL, Schrödinger
Quantum Chemistry
ORCA, Gaussian, Q-Chem, VASP, Quantum ESPRESSO, Chemcraft, Avogadro
Cheminformatics
RDKit, OpenEye, AutoDock Vina, rDock, MOLDEN, OpenBabel
Free Energy Methods
Alchemical TI, FEP (NAMD, GROMACS, FEP+), SEEKR/SEEKR2, YANK, Perses
Cryo-EM
RELION, ManifoldEM, cryoSPARC, cryoDRGN, EMAN2
Multiscale Physics
COMSOL, VCell, MCell, APBS, VESTA
AI / ML
PyTorch, TensorFlow, Keras, scikit-learn
HPC
CUDA, OpenCL, OpenMP, MPI, SLURM, PBS, LSF, AWS, Google Cloud, Azure HPC, Lustre, GPFS
Data & Visualization
Pandas, Matplotlib, Seaborn, Tableau, Gnuplot, RStudio, Jupyter, Spyder
DevOps
Git, GitHub/GitLab Actions, Docker, Singularity, Travis CI, Jenkins
Linux & Command-Line
Advanced shell scripting (Bash, AWK, Sed), Make, Cron