We use desolvation energies amino acid and atom type – of the residues present
in the interface. Selleckchem EPZ6438 The prediction is performed via two state-of-the-art classification techniques, namely linear dimensionality reduction (LDR) and support vector machines (SVM). The results on a newly compiled data set, namely BPPI, which is a joint and modified version of two well-known data sets consisting of 213 obligate and 303 non-obligate complexes, show that the best prediction is achieved with SVM (76.94% accuracy) when using desolvation energies of atom-type features. Also, the proposed approach outperforms the previous solvent accessible area-based approaches using SVM (75% accuracy) and LDR (73.06% accuracy). Moreover, a visual analysis of desolvation energies in obligate and non-obligate complexes shows that a few atom-type pairs are good descriptors for these types of complexes.”
“Purpose: AMN-107 datasheet A minority of children with Wilms tumor will experience tumor recurrence. In a previous pilot study we found an association between
expression of an immune costimulatory molecule, B7-H1, and tumor recurrence in favorable histology Wilms tumor. We sought to verify the prognostic value of B7-H1 as a biomarker in favorable histology Wilms tumor.
Materials and Methods: We performed a nested case-control study of tumors from the Fifth National Wilms Tumor Study. We randomly selected 44 children unsuccessfully treated (cases) and 49 who were successfully treated for favorable histology Wilms tumor (controls). Cases and controls were matched based on tumor stage, and the analysis was restricted to children who underwent initial resection. We excluded patients with stage IV or V disease and those treated with chemotherapy or radiation. Tumor specimens were stained for B7-H1 expression.
Results: Of the 93 total samples analyzed 60 (65%) demonstrated B7-H1 staining, with staining diffusely present in 13 (22%) and blastema predominant in 34 (57%). B7-H1 expression was associated with failure of initial therapy (p = 0.006). Patients with tumors showing less than 20% B7-H1 positive cells were at lower risk for treatment failure, while
those with tumors exhibiting greater than 60% B7-H1 positive cells were at greater risk for treatment failure. This association appeared to be independent of tumor Selleck GDC 0449 stage.
Conclusions: B7-H1 expression by favorable histology Wilms tumor is associated with an increased risk of failure of initial therapy.”
“Knowledge about protein-protein interactions (PPIs) unveils the molecular mechanisms of biological processes. However, the volume and content of published biomedical literature on protein interactions is expanding rapidly, making it increasingly difficult for interaction database curators to detect and curate protein interaction information manually. We present a multiple kernel learning-based approach for automatic PPI extraction from biomedical literature.