ArticleThe Journal of chemical physics2019
Enspara: Modeling molecular ensembles with scalable data structures and parallel computing.
Article in The Journal of chemical physics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Reduced catalytic activity of KPC β-lactamase can increase ceftazidime resistance.Communications biology · 2026Article
- The Yeh pilus adhesin is equipped with an α-helical flap motif, which contributes to pectin adherence.Science advances · 2026Article
- The G Protein Inhibitor YM-254890 is an Allosteric Glue.Journal of molecular biology · 2025Article
- Opening and closing of a cryptic pocket in VP35 toggles it between two different RNA-binding modes.eLife · 2025Article
- PathogenicThe journal of physical chemistry. B · 2025Article
- Regulation of the ordinal DNA translocation cycle in bacteriophage Φ29 through trans-subunit interactions.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Accounting for Fast vs Slow Exchange in Single Molecule FRET Experiments Reveals Hidden Conformational States.Journal of chemical theory and computation · 2024Article
- The G protein inhibitor YM-254890 is an allosteric glue.bioRxiv : the preprint server for biology · 2024Article
- Accounting for fast vs slow exchange in single molecule FRET experiments reveals hidden conformational states.bioRxiv : the preprint server for biology · 2024Article
- On Inactivation of the Coronavirus Main Protease.Journal of chemical information and modeling · 2024Article
- Toward physics-based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants.Protein science : a publication of the Protein Society · 2024Review
- PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model.Journal of chemical theory and computation · 2024Article
- Markov State Models: To Optimize or Not to Optimize.Journal of chemical theory and computation · 2024Article
- SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2023Article
- Folding@home: Achievements from over 20 years of citizen science herald the exascale era.Biophysical journal · 2023Review
- Folding@home: achievements from over twenty years of citizen science herald the exascale era.ArXiv · 2023Article
- Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network.Nature communications · 2023Article
- Article
- Structure-function correlates of fibrinogen binding byProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors.Frontiers in molecular biosciences · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Markov state models (MSMs) are quantitative models of protein dynamics that are useful for uncovering the structural fluctuations that proteins undergo, as well as the mechanisms of these conformational changes. Given the enormity of conformational space, there has been ongoing interest in identifying a small number of states that capture the essential features of a protein. Generally, this is achieved by making assumptions about the properties of relevant features-for example, that the most important features are those that change slowly. An alternative strategy is to keep as many degrees of freedom as possible and subsequently learn from the model which of the features are most important. In these larger models, however, traditional approaches quickly become computationally intractable. In this paper, we present enspara, a library for working with MSMs that provides several novel algorithms and specialized data structures that dramatically improve the scalability of traditional MSM methods. This includes ragged arrays for minimizing memory requirements, message passing interface-parallelized implementations of compute-intensive operations, and a flexible framework for model construction and analysis.
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Registered trials
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.