2019

Kernel methods for detecting coherent structures in dynamical data (preprint)

Deflation reveals dynamical structure in nondominant reaction coordinates (article, preprint, thread, press)

Variational selection of features for molecular kinetics (article, preprint)

Simultaneous coherent structure coloring facilitates interpretable clustering of scientific data by amplifying dissimilarity (article, preprint)

Energy landscapes for proteins: from single funnels to multifunctional systems (article)

Introduction to Markov state modeling with the PyEMMA software (article, preprint)

2018

PotentialNet for molecular property prediction (article, preprint, blog post)

Variational encoding of complex dynamics (articlepreprint)

Markov state models: from an art to a science (article, press)

A minimum variance clustering approach produces robust and interpretable coarse-grained models (article)

2017

Unsupervised learning of dynamical and molecular similarity using variance minimization (preprint)

Note: MSM lag time cannot be used for variational model selection (article, preprint)

Modeling the mechanism of CLN025 beta-hairpin formation (articlepreprint, first blog post, second blog post)

Ward clustering improves cross-validated Markov state models for protein folding (article)

Identification of simple reaction coordinates from complex dynamics (article, preprint)

MSMBuilder: Statistical models for biomolecular dynamics (article, preprint)

2016

Osprey: Hyperparameter optimization for machine learning (article)

Optimized parameter selection reveals trends in Markov state models for protein folding (article)

Impurity effects on solid-solid transitions in atomic clusters (article)*

2012

Ancient Greek accent windows (article)

Post-peninitial accent in Kashaya (article)

 

* Erdös number: 3 (Husic < Wales < Salamon < Erdös)

Husic, Schebarchov, & Wales

Salamon, Wales & others

Salamon & Erdös