Posts Tagged ‘gpmtg’

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human: Cell

February 24, 2017

FissionNet: Proteome-wide [pombe] Interactome Reveals #Network Evolution Principles
http://www.Cell.com/cell/abstract/S0092-8674(15)01556-1 Involving ~1300 soluble proteins

Protein-structure-guided discovery of functional mutations across 19 cancer types : Nature Genetics : Nature Research

December 11, 2016

Protein-structure-guided discovery of functional mutations across 19 #cancer types http://www.nature.com/ng/journal/v48/n8/abs/ng.3586.html Cancer3D relates SNVs to drugs

http://www.nature.com/ng/journal/v48/n8/abs/ng.3586.html

Skhizein: a really nice animation on today’s grpmtg

December 9, 2016

https://vimeo.com/36824575

PLOS Computational Biology: PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

November 28, 2016

PredictSNP…Consensus Classifier for Prediction of Disease-Related
Mutations http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003440 Demo of various #ensemble approaches

Frustration in biomolecules | Quarterly Reviews of Biophysics | Cambridge Core

November 1, 2016

#Frustration in biomolecules
https://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/frustration-in-biomolecules/DECEA176849986FC11DB079C1EB4B24A Reviews the field: how large molecules pay a local price to achieve global stability

PLOS Computational Biology: PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

October 9, 2016

PredictSNP2: A Unified Platform http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004962 Ensembles many scores for the impact of non-coding variants, including #FunSeq

Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles

September 30, 2016

Elucidating Molecular Motion (compatible w. #NMR relaxation times) through…Filters of Energy-Minimized…Ensembles
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983377

Predicting peptide binding sites on protein surfaces by clustering chemical interactions – Yan – 2014 – Journal of Computational Chemistry – Wiley Online Library

July 4, 2016

Predicting peptide binding sites on protein surfaces by ACCLUSTER http://onlinelibrary.wiley.com/doi/10.1002/jcc.23771/abstract #Chemical interactions out perform pure #packing

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences: Cell

April 24, 2016

Learning the…Determinants of Alternative #Splicing [in a largely linear model] from Millions of Random Sequences
http://www.cell.com/cell/abstract/S0092-8674(15)01271-4

** Rosenberg et al Cell. 2015

Builds a model of splicing using a library of randomized sequence Also, builds a generalized model for predicting effect of a SNP in the Geuvadis RNAseq
7mer model does well with lots of data

Protein folds recognized by an intelligent predictor based-on evolutionary and structural information – Cheung – 2015 – Journal of Computational Chemistry – Wiley Online Library

April 17, 2016

Fold [class] recognized by an…[NN] predictor based-on evolutionary & structural info., w/ particle-swarm training
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24232/full

Ngaam J. Cheung,
Xue-Ming Ding,
Hong-Bin Shen

First published: 27 October 2015
DOI: 10.1002/jcc.24232