Models and Web Resources

CAMV: The Computer-Assisted Manual Validation (CAMV) tool expedites the manual validation process for LC-MSMS data as well as collects and summarizes quantitative information from iTRAQ or SILAC experiments.

DrugComboOptHetTumor: Drug combination optimization for Monte Carlo sampled heterogeneous tumor populations, with statistical and sensitivity analyses on simulation results. Supplemental MATLAB codes for Intratumor Heterogeneity Alters Most Effective Drugs in Designed Combinations, which examines 1) how heterogeneity affects the utility of drug combinations, and 2) how current clinical practice of tumor diagnosis, which biases toward focus on the predominant subpopulation, affects design of drug combinations.

The MIT/ICBP siRNA Database: An on-line database of experimentally validated siRNAs and shRNAs against target genes, with a focus on genes thought to be involved in cancer.

NetPhorest: NetPhorest integrates in vitro kinase and phosphopeptide-binding domain specificity assays with publically accessible known in vivo substrate lists in order to generate substrate specificity descriptions for individual proteins as well as protein families.

NetworKIN: NetworKIN predicts the kinase responsible for sites of protein phosphorylation using motif analysis to identify the likely kinase family, and then protein-protein interaction network analysis to identify the most likely individual kinase.

phoMSVal: phoMSVal is an open-source platform developed for managing MS/MS data and automatically validating identified phosphopeptides.

PTMScout: PTMScout is a tool for viewing and analyzing high-throughput post-translational modification proteomic data, with a particular eye towards novel hypothesis generation.

Q2LM: Querying Quantitative Logic Models (Q2LM) is a MATLAB library that uses constrained fuzzy logic models based on prior knowledge networks to address two questions about a biological system: 1) What perturbation results in a specified downstream effect? and 2) In what environments do those perturbations produce that effect?

Scansite: Scansite contains substrate specificity matrices determined by in vitro peptide library experiments for a number of kinases and phosphopeptide-binding domains.  These are used to predict likely interactors with putative substrate sequences of interest.