Invalid SMILES are Beneficial Rather than Detrimental to Chemical Language Models
Skinnider (2024) shows that generating invalid SMILES actually improves chemical language model performance through …...
Computational Chemistry
Synthetic Isomer Data Generation Pipeline
An end-to-end cheminformatics pipeline transforming 1D chemical formulas into 3D conformer datasets using graph …...
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 …
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 …
Mini-Protein Trajectory Generation
Automated GROMACS pipeline generating high-fidelity MD trajectories with atomic force extraction for Neural Network …...