ArticleJournal of chemical information and modeling2023
LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- A Minimalist Model for Navigating Conformational Landscape Uncovers the Activation Mechanism of βACS physical chemistry Au · 2026Article
- Pathway representationDigital discovery · 2026Article
- Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways.bioRxiv : the preprint server for biology · 2026Article
- Rapid estimation of protein folding pathways from sequence alone using AlphaFold2.Nature communications · 2025Article
- SHINE: Deterministic Many-to-Many Clustering of Molecular Pathways.Journal of chemical information and modeling · 2025Article
- Molecular simulations reveal intricate coupling between agonist-bound β-adrenergic receptors and G protein.iScience · 2025Article
- PathInHydro, a Set of Machine Learning Models to Identify Unbinding Pathways of Gas Molecules in [NiFe] Hydrogenases.Journal of chemical information and modeling · 2025Article
- Gating residues govern ligand unbinding kinetics from the buried cavity in HIF-2α PAS-B.Protein science : a publication of the Protein Society · 2024Article
- AlphaFold2bioRxiv : the preprint server for biology · 2024Article
- Layer-by-layer unsupervised clustering of statistically relevant fluctuations in noisy time-series data of complex dynamical systems.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.Journal of chemical information and modeling · 2024Article
- Revisiting Textbook Azide-Clock Reactions: A "Propeller-Crawling" Mechanism Explains Differences in Rates.Journal of the American Chemical Society · 2024Article
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Abstract
The pathways by which a molecular process transitions to a target state are highly sought-after as direct views of a transition mechanism. While great strides have been made in the physics-based simulation of such pathways, the analysis of these pathways can be a major challenge due to their diversity and variable lengths. Here, we present the LPATH Python tool, which implements a semiautomated method for linguistics-assisted clustering of pathways into distinct classes (or routes). This method involves three steps: 1) discretizing the configurational space into key states, 2) extracting a text-string sequence of key visited states for each pathway, and 3) pairwise matching of pathways based on a text-string similarity score. To circumvent the prohibitive memory requirements of the first step, we have implemented a general two-stage method for clustering conformational states that exploits machine learning. LPATH is primarily designed for use with the WESTPA software for weighted ensemble simulations; however, the tool can also be applied to conventional simulations. As demonstrated for the C7
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.