Posts Tagged ‘mutation’

ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma: Cancer Cell

May 22, 2015

ALK Mutations Confer Differential Oncogenic Activation
http://www.cell.com/cancer-cell/abstract/S1535-6108%2814%2900393-6 MD modeling better assessing #SNV impact than stats, ie sift

ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma

Scott C. Bresler
Daniel A. Weiser
Peter J. Huwe

Ravi Radhakrishnan
Mark A. Lemmon
Yaël P. Mossé

DOI: http://dx.doi.org/10.1016/j.ccell.2014.09.019

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nature Methods (2010) 7: 248-249.

October 11, 2014

Server for predicting damaging missense #mutations
http://www.nature.com/nmeth/journal/v7/n4/full/nmeth0410-248.html Polyphen2 uses both structure & sequence (eg ASA & conservation)

http://www.ncbi.nlm.nih.gov/pubmed/20354512

Polyphen2 includes both structural and sequence features to predict the effect of nonsynonymous substitutions on protein function. Similar to many other methods, Polyphen2 uses evolutionary conservation as one of the features to identify functionally important residues. Integration of 3D-structure, membrane-specific features (PHAT matrix for TM regions) and other features such as protein-domain and active-site are the strengths of Polyphen2 compared to other sequence-based software making it a good tool for prediction.