PRAG1
PEAK1 related, kinase-activating pseudokinase 1
Kinase Domain Structure:
- Title: Crystal structure of Sugen kinase 223
- Resolution: 2.95
Associated Compounds:
- NA
View This Structure on RCSB PDB
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system drawing from natural language processing systems and structured databases. It collects mechanistic and causal assertions, represents them in a standardized form (INDRA Statements), and assembles them into various modeling formalisms including causal graphs and dynamical models. More information on this work can be found on Github. In this particular figure, several interaction-types are depicted; physical complexes (blue), phosphorylation (black), and general up- or downregulation (green and red, respectively). Biomacromolecules are represented as squares, small molecule as circles, and biological processes and diamonds. The thickness of each line reflects a confidence score, with thicker lines higher in confidence.
The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
- https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
- http://clinchem.aaccjnls.org/content/50/4/732
- “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)
View Peptide Parameters
The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
- https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
- http://clinchem.aaccjnls.org/content/50/4/732
- “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)
View Peptide Parameters
The Reactome Knowledgebase of Human Biological Pathways and Processes is a curated and peer-reviewed knowledgebase available online as an open access resource that can be freely used and distributed by all members of the biological research community. This view of the reactome database is focused on PRAG1 and displays the pathways associated with PRAG1.