2016-08-30 A recent publication in PNAS describes a VCell model developed as collaboration between the Rangamini group at UC Davis and the Oster lab at UC Berkeley. The model couples biochemical signaling machinery with actin remodeling events in the dendritic spine; view the details on our Published Models list.
2016-07-27 A new publication from Sayak Bhattacharya and Pablo Iglesias at Johns Hopkins University describes the step-by-step construction of dynamical models of chemotactic networks using VCell (Bhattacharya and Iglesias 2016. Methods Mol. Biol. 1407:397, PMID 27271916). Publically available VCell models associated with the paper can be found on our list of published models here.
2016-07-15 VCell models were used to test possible mechanisms for maintenance of subcellular microdomains of cAMP in cardiomyocytes in a recent publication in PLoS Computational Biology by Yang et al. Find the publication and details of the models on our Published Models listing.
2016 -06-09 Hysteresis-like binding of coagulation factors x/xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization (Podoplelova et al. 2016. Biochim Biophys Acta. 1858:1216-1227. PMID 26874201). Find the public BioModel here.
VCell models were used to quantitatively analyze FRET measurements were used to demonstrate that voltage-sensing phosphatases (VSPs) have catalytic activity for PIP3 (Keum et al. 2016. Phosphoinositide 5- and 3-phosphatase activities of a voltage-sensing phosphatase in living cells show identical voltage dependence. Proc Natl Acad Sci U S A. 10.1073/pnas.1606472113, PMID 27222577). Find the public VCell model here.
2016-05-03 A new model of pancreatic beta cell G-protein coupled receptors and second messenger interactions was recently published in PLoS One by Fridlyand and Philipson. Go to our Published Models listing to link to the publication and view details of the model.
2016-03-01. A new publication describes a VCell model that evaluates the contributions of protein kinases and beta-arrestin to termination of protease-activated receptor 2 signaling. Visit the Published Models page for details and links to the publication.
2016-02-02 SpringSaLad (Springs, Sites, and Langevin Dynamics) is a new software that uses a course-grained approach to model biomolecules as a group of linked spherical sites with excluded volumes. The software user material is available here. Read about the method and software in Springsalad: A spatial, particle-based biochemical simulation platform with excluded volume. Michalski, P.J., and L.M. Loew. 2016 Biophys J. 110:523-529. PMID 26840718.