ArticleThe journal of physical chemistry. B2017
SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- A theoretical framework for random acceleration molecular dynamics simulations.The Journal of chemical physics · 2026Article
- A Multiscale Simulation Approach to Compute Protein-Ligand Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics.Journal of chemical information and modeling · 2025Article
- Simultaneous Construction of Free Energy Surfaces via Multisite λ Dynamics and Umbrella Sampling.Journal of chemical theory and computation · 2025Article
- Toward Grid-Based Models for Molecular Association.Journal of chemical theory and computation · 2025Article
- Design, optimization, and ADMET evaluation of S11a-0000168202: A promising LIMK1 inhibitor for gastric cancer treatment.PloS one · 2025Article
- 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
- Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.Expert opinion on drug discovery · 2024Review
- Quantitative Prediction of Dissociation Rates of PYK2 Ligands Using Umbrella Sampling and Milestoning.Journal of chemical theory and computation · 2024Article
- QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.Chemical science · 2023Article
- Free energy along drug-protein binding pathways interactively sampled in virtual reality.Scientific reports · 2023Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- 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
- Article
- Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling.Quarterly reviews of biophysics · 2023Review
- SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.Journal of chemical information and modeling · 2022Article
- Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution.Journal of chemical theory and computation · 2022Article
- GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems.Journal of chemical information and modeling · 2022Article
- Accelerating All-Atom Simulations and Gaining Mechanistic Understanding of Biophysical Systems through State Predictive Information Bottleneck.Journal of chemical theory and computation · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We present the Simulation Enabled Estimation of Kinetic Rates (SEEKR) package, a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory. To demonstrate its utility, we compute the k
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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.