GDB-17: Chemical Universe Database (166B Molecules)
Dataset card for GDB-17, containing 166 billion small organic molecules representing the largest enumerated chemical …
Computational-Chemistry
GEOM Dataset: 3D Molecular Conformer Generation
Learn how GEOM transforms 2D molecular graphs into dynamic 3D conformer ensembles for molecular machine learning …
Can You Hear the Shape of a Molecule? (Part Three)
Supervised learning reveals hidden eigenvalue patterns that clustering missed, testing k-NN and logistic regression on …
Can You Hear the Shape of a Molecule? (Part Two)
Clustering analysis reveals why Coulomb matrix eigenvalues struggle with larger alkanes, using Dunn Index and silhouette …
Can You Hear the Shape of a Molecule?
Explore molecular shape recognition using Coulomb matrix eigenvalues. Analysis of alkane isomers from data generation to …
Understanding Coulomb Matrices for Molecular Machine Learning
Learn how Coulomb matrices encode 3D molecular structure for machine learning—from basic theory to Python implementation …
Kabsch Algorithm: NumPy, PyTorch, TensorFlow, and JAX
Learn about the Kabsch algorithm for optimal point alignment with implementations in NumPy, PyTorch, TensorFlow, and JAX …
Copper Adatom Diffusion on Cu(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation of copper adatom diffusion on a Cu(100) surface, showing atomic mobility …
LAMMPS Tutorial: Copper Adatom Diffusion
LAMMPS tutorial for copper surface diffusion simulation and ML training data generation. Includes setup, analysis, and …
Platinum Adatom Diffusion on Pt(100) Surface
LAMMPS tutorial for platinum adatom diffusion simulation and ML training data. Learn how heavier atoms behave …
Platinum Adatom Diffusion on Pt(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation of platinum adatom diffusion on a Pt(100) surface, showing atomic mobility …
Generating Mini-Protein Trajectories with GROMACS
Systematic GROMACS workflows for simulating mini-proteins across multiple amino acids to generate diverse MD …