Posts Tagged ‘ismb’

Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction — ScienceDirect

July 19, 2014

Dunbrack PhD thesis
http://www.sciencedirect.com/science/article/pii/S0022283683711708?via=ihub Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction — ScienceDirect

Conformational Optimization with Natural Degrees of Freedom: A Novel Stochastic Chain Closure Algorithm

July 19, 2014

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119633/

Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures

July 19, 2014

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2692023/

Maps of protein structure space reveal a fundamental relationship between protein structure and function

July 19, 2014

Maps of protein structure space reveal a fundamental relationship between protein structure and function
http://www.pnas.org/content/108/30/12301.abstract

Mapping functional transcription factor networks from gene expression data

July 19, 2014

Mapping functional transcription factor networks from gene expression data

NetProphet ref

http://genome.cshlp.org/content/23/8/1319.long

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

July 19, 2014

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data
http://nar.oxfordjournals.org/content/early/2014/01/24/nar.gkt1411.full

Exploring mechanisms of human disease through structurally resolved protein interactome networks

July 19, 2014

Mol Biosyst. Author manuscript; available in PMC Jul 1, 2014. Published in final edited form as:
Mol Biosyst. Jan 2014; 10(1): 9–17.
doi: 10.1039/c3mb70225a

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4061614/

Three-dimensional reconstruction of protein networks provides insight into human genetic disease : Nature Biotechnology : Nature Publishing Group

July 19, 2014

http://www.nature.com/nbt/journal/v30/n2/full/nbt.2106.html

Dissecting Disease Inheritance Modes in a Three-Dimensional Protein Network Challenges the “Guilt-by-Asso ciation” Principle

July 19, 2014

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710751/

surprisingly, no positional effects on LOF mutations … significant proportion of truncation alleles give rise to functional products

“guilt by assoc works”

signif. number dom mut give rise to func products

chinese cancer data

July 18, 2014

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759719/

Annotated somatic variants and interactive variant analysis results are available online atwww.ingenuity.com/acrg2012.

Eighty-eight primary HCC tumors and matched adjacent nontumor liver tissues were analyzed by whole-genome DNA sequencing to identify somatic mutations and HBV integration sites. The vast majority (92%,n = 81) of patients in this cohort were HBV carriers (i.e., HBsAg seropositive) suffering from chronic hepatitis B or cirrhosis. None of the patients were hepatitis C virus (HCV) positive

the data:

http://gigadb.org/dataset/100034

The original paper is here: http://www.ncbi.nlm.nih.gov/pubmed/23788652