ArticleBiophysical journal2016
SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling.Biophysical journal · 2026Article
- CASPULE: A computational tool to study sticker spacer polymer condensates.PLoS computational biology · 2026Article
- Models of Cellular Mechanosensation.Results and problems in cell differentiation · 2026Review
- Biomolecular Phase Boundaries are Described by a Solubility Product That Accounts for Variable Stoichiometry and Soluble Oligomers.Journal of the American Chemical Society · 2025Article
- CASPULE: A computational tool to study sticker spacer polymer condensates.bioRxiv : the preprint server for biology · 2025Article
- Biomolecular phase boundaries are described by a solubility product that accounts for variable stoichiometry and soluble oligomers.bioRxiv : the preprint server for biology · 2025Article
- Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling.bioRxiv : the preprint server for biology · 2025Article
- Parallelization of Particle-Based Reaction-Diffusion Simulations Using MPI.Journal of computational chemistry · 2025Article
- Measurement of solubility product reveals the interplay of oligomerization and self-association for defining condensate formation.Molecular biology of the cell · 2024Article
- Measurement of solubility product in a model condensate reveals the interplay of small oligomerization and self-association.bioRxiv : the preprint server for biology · 2024Article
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- Building the next generation of virtual cells to understand cellular biology.Biophysical journal · 2023Review
- Implications of different membrane compartmentalization models in particle-basedRoyal Society open science · 2023Article
- MolClustPy: a Python package to characterize multivalent biomolecular clusters.Bioinformatics (Oxford, England) · 2023Article
- The maximum solubility product marks the threshold for condensation of multivalent biomolecules.Biophysical journal · 2023Article
- Dissecting the general mechanisms of protein cage self-assembly by coarse-grained simulations.Protein science : a publication of the Protein Society · 2023Article
- Particle-based model of mechanosensory contractility kit assembly.Biophysical journal · 2022Article
- MVsim is a toolset for quantifying and designing multivalent interactions.Nature communications · 2022Article
- On the formation of ordered protein assemblies in cell-cell interfaces.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Robustness and the evolution of length control strategies in the T3SS and flagellar hook.Biophysical journal · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
We introduce Springs, Sites, and Langevin Dynamics (SpringSaLaD), a comprehensive software platform for spatial, stochastic, particle-based modeling of biochemical systems. SpringSaLaD models biomolecules in a coarse-grained manner as a group of linked spherical sites with excluded volume. This mesoscopic approach bridges the gap between highly detailed molecular dynamics simulations and the various methods used to study network kinetics and diffusion at the cellular level. SpringSaLaD is a standalone tool that supports model building, simulation, visualization, and data analysis, all through a user-friendly graphical user interface that should make it more accessible than tools built into more comprehensive molecular dynamics infrastructures. Importantly, for bimolecular reactions we derive an exact expression relating the macroscopic on-rate to the various microscopic parameters with the inclusion of excluded volume; this makes SpringSaLaD more accurate than other tools, which rely on approximate relationships between these parameters.
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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.