Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data

Abstract

Supplementary data are available at Bioinformatics online.

Co-expression of KLK6 and KLK10 as prognostic factors for survival in pancreatic ductal adenocarcinoma

“…By means of these methods we could identify four potential interaction partners for KLK6: a-1 antiproteinase, AT III, pigment epithelium-derived factor and synuclein (Table 3). However, no additional interaction partner for KLK10 other than the already described could be identified (Dawelbait et al, 2007).…”

“…To find possible novel interactions we used structure-and sequence-based prediction of protein interactions as described earlier (Altschul et al, 1997;Mishra et al, 2006;Dawelbait et al, 2007).…”

Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

“…Aytuna et al 11 presented a structure-based method to predict protein–protein interactions using known template interfaces; if surface regions of two proteins are structurally similar to the two sides of a template interface, the two proteins are predicted to interact. More recently, Schroeder and co-workers 6 used structural templates to predict novel protein interactions specific for pancreatic cancer. Several groups have also shown how it is possible to estimate kinetic constants for the binding parameters using structural information.…”

Targeting the Protein Quality Control (PQC) Machinery

“…Clinical testing of brivudine in combination with gemcitabine and cisplatin in pancreatic cancer patients improves the efficiency of chemotherapy [36]. The effect of brivudine may be due to down-regulation of Hsp27 activity in tumor cells [37], although other molecular targets are proposed [38]. Affinity chromatography with brivudine-loaded magnetic beads pulls down only Hsp27.…”