Programming
Python, Bash, AWK, MATLAB, R, Mathematica, LaTeX
Molecular Simulation
AMBER, 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+, SEEKR/SEEKR2, YANK, Perses
Cryo-EM
RELION, ManifoldEM, cryoSPARC, cryoDRGN, EMAN2
AI / ML
PyTorch, TensorFlow, Keras, scikit-learn
HPC
CUDA, OpenMP, MPI, SLURM, PBS, AWS, Google Cloud, Azure HPC, Lustre, GPFS
Data & Visualization
Pandas, Matplotlib, Seaborn, Tableau, Gnuplot, Jupyter
DevOps
Git, GitHub Actions, Docker, Singularity, Travis CI, Jenkins