Internal coarse-graining of molecular systems
Modelers of molecular signaling networks must cope with the combinatorial explosion of
protein states generated by posttranslational modifications and complex formation. Rule …
protein states generated by posttranslational modifications and complex formation. Rule …
Ligand‐dependent responses of the ErbB signaling network: experimental and modeling analyses
MR Birtwistle, M Hatakeyama, N Yumoto… - Molecular systems …, 2007 - embopress.org
Deregulation of ErbB signaling plays a key role in the progression of multiple human
cancers. To help understand ErbB signaling quantitatively, in this work we combine …
cancers. To help understand ErbB signaling quantitatively, in this work we combine …
Rule‐based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems
Rule‐based modeling was developed to address the limitations of traditional approaches for
modeling chemical kinetics in cell signaling systems. These systems consist of multiple …
modeling chemical kinetics in cell signaling systems. These systems consist of multiple …
[HTML][HTML] Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops
A Kiyatkin, E Aksamitiene, NI Markevich… - Journal of biological …, 2006 - ASBMB
Grb2-associated binder 1 (GAB1) is a scaffold protein involved in numerous interactions that
propagate signaling by growth factor and cytokine receptors. Here we explore in silico and …
propagate signaling by growth factor and cytokine receptors. Here we explore in silico and …
Scalable simulation of cellular signaling networks
Given the combinatorial nature of cellular signalling pathways, where biological agents can
bind and modify each other in a large number of ways, concurrent or agent-based …
bind and modify each other in a large number of ways, concurrent or agent-based …
[HTML][HTML] Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding
LB Kleiman, T Maiwald, H Conzelmann… - Molecular cell, 2011 - cell.com
Epidermal growth factor receptors (ErbB1–4) are oncogenic receptor tyrosine kinases
(RTKs) that regulate diverse cellular processes. In this study, we combine measurement and …
(RTKs) that regulate diverse cellular processes. In this study, we combine measurement and …
[HTML][HTML] Quantitative immunology for physicists
The adaptive immune system is a dynamical, self-organized multiscale system that protects
vertebrates from both pathogens and internal irregularities, such as tumors. For these …
vertebrates from both pathogens and internal irregularities, such as tumors. For these …
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
BRAF is prototypical of oncogenes that can be targeted therapeutically and the treatment of
BRAFV600E melanomas with RAF and MEK inhibitors results in rapid tumor regression …
BRAFV600E melanomas with RAF and MEK inhibitors results in rapid tumor regression …
Systems chemical biology
The increasing availability of data related to genes, proteins and their modulation by small
molecules has provided a vast amount of biological information leading to the emergence of …
molecules has provided a vast amount of biological information leading to the emergence of …
Dimerization of VEGF receptors and implications for signal transduction: a computational study
F Mac Gabhann, AS Popel - Biophysical chemistry, 2007 - Elsevier
Vascular endothelial growth factor (VEGF) is a potent cytokine involved in the induction of
neovascularization. Secreted as a cysteine-linked dimer, it has two binding sites at opposite …
neovascularization. Secreted as a cysteine-linked dimer, it has two binding sites at opposite …