Posts Tagged ‘j0mg’

Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data: Biophysical Journal

August 18, 2018

Modeling RNA Secondary Structure with Sequence Comparison &
Experimental Mapping Data
https://www.Cell.com/biophysj/fulltext/S0006-3495(17)30689-6 combines TurboFold sec. structure prediction w/ results of SHAPE assays

Zhen Tan
Gaurav Sharma
David H. Mathews

Open Archive Published:July 20, 2017
DOI:https://doi.org/10.1016/j.bpj.2017.06.039

How to sail smoothly from academia to industry

April 21, 2018

How to sail smoothly from academia to industry
http://www.nature.com/articles/d41586-018-03306-1 Teamwork is key. Perhaps this should be emphasized more in graduate training? #Jobs QT:{{”
“When immuno-oncologist Martijn Bijker decided to move from academia to industry, he asked a friend to review his CV. His friend — who had worked in the pharmaceutical sector for two decades — told him to relegate his lists of publications, posters and presentations to the back of the document. The focus, he said, should be on teamwork skills and the ability to perform the job requirements.”
“}}

Multistep nucleation of nanocrystals in aqueous solution : Nature Chemistry : Nature Research

October 1, 2017

Multistep nucleation of nanocrystals in…solution
http://www.Nature.com/nchem/journal/v9/n1/full/nchem.2618.html Creation of Au-Au pair, expelling water, drives cluster formation

QT:{{”
To explain how the gold-rich aqueous phase forms and breaks down in Figures 1A and 2A, we
performed ab-initio calculations of a hydrated gold atom pair (Figure 4). This hydrated atom pair
becomes ionized when brought closer together: the left gold atom plus two nearby water molecules
form a linear cationic coordination complex, [Au(H2O)2]+1, while the right gold atom becomes an
anion surrounded by a simple hydration shell. Other (square planar and linear) complexes involving
chloride and hydroxide ligands may also participate, depending on pH (26, 33) (Section SI2). For
nanoclusters to form inside the gold-rich aqueous phase, pairs of gold atoms within it must be partially
dehydrated. In our calculations (Figure 4), this dehydration is delayed by a 7.6 kcal/mol (12.9 kBT)
energy barrier required to breakdown the linear cationic complex (close to the gold anion).
“}}

also:
https://arxiv.org/abs/1605.04632

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

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

PLOS Computational Biology: Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations

December 18, 2015

Folding by Chaperones Accelerates Evolutionary Dynamics
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003269 Multiscale models link NT mutations, PPIs & cell populations

Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes: Origins of Affinity and Selectivity: Biophysical Journal

November 15, 2015

#Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes http://www.cell.com/biophysj/abstract/S0006-3495(14)00928-X Non-human selectivity studied w. coarse-grained MD