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Rules for Modeling Signal-Transduction Systems
Approaches to creation of mathematical models of signaling systems with strategies that keep the models from being unwieldy but still allow them to accurately reflect biological systems are reviewed.
Flow cytometric analysis of transmembrane phospholipid movement in bull sperm.
A simple model of NBD-phospholipid equilibria was developed and fit to the kinetic data and reflected major features of the experimental data and provide a potential tool for predicting the dynamics of endogenous lipids.
Simulation of large-scale rule-based models
DYNSTOC enables the simulation of rule-based models that cannot be simulated by conventional methods and is demonstrated to simulate models accounting for multisite phosphorylation and multivalent binding processes that are characterized by large numbers of reactions.
Targeting the tumor microenvironment in cancer: why hyaluronidase deserves a second look.
The role of HA in cancer, methods of targeting HA, and clinical studies performed to date are described, and it is proposed that targeting HA could now be an effective treatment option for patients with many different types of solid tumors.
Real-time analysis of the assembly of ligand, receptor, and G protein by quantitative fluorescence flow cytometry.
This work has characterized a family of fluoresceinated formyl peptides and analyzed both steady-state and dynamic aspects of ligandformyl peptide-receptor interactions in digitonin-permeabilized human neutrophils.
Hypoxia triggers hedgehog-mediated tumor-stromal interactions in pancreatic cancer.
It is suggested that increased HIF-1α produced by hypoxic tumors triggers the desmoplasic reaction in pancreatic cancer, which is then amplified by a feed forward loop involving cycles of decreased blood flow and increased hypoxia.
AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina
Implementation of XBSF into AutoDock Vina has been shown to improve the accuracy of the docking result with regards to halogenated ligands, thus effectively lowering the output RMSD values.