ArticleBioinformatics (Oxford, England)2018
mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling.Biophysical journal · 2026Article
- Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling.bioRxiv : the preprint server for biology · 2025Article
- MVsim is a toolset for quantifying and designing multivalent interactions.Nature communications · 2022Article
- Article
- The Interplay of Structural and Cellular Biophysics Controls Clustering of Multivalent Molecules.Biophysical journal · 2019Article
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Authors and funding
4 authors.
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Abstract
Motivation: Proteins, especially those involved in signaling pathways are composed of functional modules connected by linker domains with varying degrees of flexibility. To understand the structure-function relationships in these macromolecules, it is helpful to visualize the geometric arrangement of domains. Furthermore, accurate spatial representation of domain structure is necessary for coarse-grain models of the multi-molecular interactions that comprise signaling pathways. Results: We introduce a new tool, mol2sphere, that transforms the atomistic structure of a macromolecule into a series of linked spheres corresponding to domains. It does this with a k-means clustering algorithm. It may be used for visualization or for coarse grain modeling and simulation. Availability and implementation: PyMOL plugin, source, and documentation. https://nmrbox.org/registry/mol2sphere. SpringSaLaD executables and documentation: http://vcell.org/ssalad, SpringSaLaD v.2 source: https://github.com/jmasison/SpringSaLaD.
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