Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling
Summary of Torrie and Valleau's 1977 paper that introduces Umbrella Sampling, a powerful and general importance sampling technique for overcoming the …
Computational-Chemistry
12 posts tagged with computational-chemistry.
Processes of Adsorption and Diffusion on Solid Surfaces
Summary of Lennard-Jones's 1932 paper introducing a potential energy surface model to unify physical and chemical adsorption, explaining the concept …
The Number of Isomeric Hydrocarbons of the Methane Series
Summary of Henze and Blair's seminal 1931 JACS paper introducing a recursive method for calculating the number of structural isomers of alkanes, …
MARCEL Dataset Card
A comprehensive dataset card for the MoleculAR Conformer Ensemble Learning (MARCEL) benchmark - the first comprehensive benchmark for learning from …
GDB-13 Dataset Card
A dataset card for the Generated Database 13 (GDB-13), a database of nearly 1 billion small organic molecules for virtual screening and drug …
GEOM Dataset Card
A comprehensive dataset card for the Geometric Ensemble Of Molecules (GEOM) dataset - 37 million energy-annotated molecular conformations for machine …
970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13
A summary of the 2009 JACS paper by Blum and Reymond introducing the GDB-13 database, an enumeration of nearly one billion druglike small molecules …
Beyond 2D: Exploring the GEOM Dataset for 3D Molecular Conformer Generation
Learn how GEOM transforms 2D molecular graphs into dynamic 3D conformer ensembles for molecular machine learning applications.
Can You Hear the Shape of a Molecule? (Part Three)
Analysis of molecular shape recognition: using supervised learning to test if labels can reveal patterns in Coulomb matrix eigenvalues.
Can You Hear the Shape of a Molecule? (Part Two)
Unsupervised clustering analysis shows why Coulomb matrix eigenvalues struggle with larger alkanes—with separability metrics.
Can You Hear the Shape of a Molecule?
Explore molecular shape recognition using Coulomb matrix eigenvalues. Analysis of alkane isomers from data generation to classification limits.
Learning About Coulomb Matrices for Molecular ML
Learn about Coulomb matrices for molecular ML: understand how they encode 3D structure, why they're rotation-invariant, and their practical …