2008/12/25 by Jin Yang, Yang, Jin, William S. Hlavacek +1 · 1 citation
Biochemistry, Genetics and Molecular Biology · Computer Science · #Computational Drug Discovery Methods #FOS: Biological sciences #Gene Regulatory Network Analysis #Molecular Networks (q-bio.MN) #Quantitative Methods (q-bio.QM) #Receptor Mechanisms and Signaling #q-bio.MN #q-bio.QM
paper · pdf · doi:10.48550/arxiv.0812.4619
18 pages, 6 figures
openalex publication_date 2008/12/25 · arxiv created 2010/03/04 · arxiv updated 2010/03/05 · openalex created_date 2016/06/24 · openalex updated_date 2026/07/28
The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient when simulating aggregation processes with large biomolecular complexes. Here, we present a rejection-free method for determining the kinetics of multivalent biomolecular interactions, and we apply the method to simulate simple models for ligand-receptor interactions. Simulation results show that performance of the rejection-free method is equal to or better than that of the rejection method over wide parameter ranges, and the rejection-free method is more efficient for simulating systems in which aggregation is extensive. The rejection-free method reported here should be useful for simulating a variety of systems in which multisite molecular interactions yield large molecular aggregates.