ArticleJournal of chemical information and modeling2022
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 41 citations in OpenAlex.
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- Advances and Challenges in Milestoning Simulations for Drug-Target Kinetics.Journal of chemical theory and computation · 2024Article
- Prediction of Threonine-Tyrosine Kinase Receptor-Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics.The journal of physical chemistry letters · 2024Article
- Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.Journal of chemical theory and computation · 2024Article
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- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- Quantitative Prediction of Dissociation Rates of PYK2 Ligands Using Umbrella Sampling and Milestoning.Journal of chemical theory and computation · 2024Article
- Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.Mini reviews in medicinal chemistry · 2024Review
- QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.Chemical science · 2023Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
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- Flexible Topology: A Dynamic Model of a Continuous Chemical Space.Journal of chemical theory and computation · 2023Article
- Predicting Biomolecular Binding Kinetics: A Review.Journal of chemical theory and computation · 2023Review
- Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations.Journal of chemical information and modeling · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present SEEKR2 (simulation-enabled estimation of kinetic rates version 2)─the latest iteration in the family of SEEKR programs for using multiscale simulation methods to computationally estimate the kinetics and thermodynamics of molecular processes, in particular, ligand-receptor binding. SEEKR2 generates equivalent, or improved, results compared to the earlier versions of SEEKR but with significant increases in speed and capabilities. SEEKR2 has also been built with greater ease of usability and with extensible features to enable future expansions of the method. Now, in addition to supporting simulations using NAMD, calculations may be run with the fast and extensible OpenMM simulation engine. The Brownian dynamics portion of the calculation has also been upgraded to Browndye 2. Furthermore, this version of SEEKR supports hydrogen mass repartitioning, which significantly reduces computational cost, while showing little, if any, loss of accuracy in the predicted kinetics.
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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.