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
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).
“}}
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
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
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 http://www.cell.com/biophysj/abstract/S0006-3495(14)00928-X Non-human selectivity studied w. coarse-grained MD