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Article
Open AccessModulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core
Controlled modulation of nucleosomal DNA accessibility via post-translational modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs in the globular histone core—including...
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Chapter
Modeling of Signal Transduction by the Quorum-Sensing Pathway in the Vibrios
Several bacterial species have regulatory networks that enable global alterations in gene expression in response to changes in local cell density. This process, commonly referred to as quorum sensing, typicall...
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Article
The SAMPL4 host–guest blind prediction challenge: an overview
Prospective validation of methods for computing binding affinities can help assess their predictive power and thus set reasonable expectations for their performance in drug design applications. Supramolecular ...
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Article
Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method
Accurate methods for predicting protein–ligand binding affinities are of central interest to computer-aided drug design for hit identification and lead optimization. Here, we used the mining minima (M2) method...
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Article
The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations
We used blind predictions of the 47 hydration free energies in the SAMPL4 challenge to test multiple partial charge models in the context of explicit solvent free energy simulations with the general AMBER forc...
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Protocol
Systems Biology of Microbial Communities
Microbes exist naturally in a wide range of environments in communities where their interactions are significant, spanning the extremes of high acidity and high temperature environments to soil and the ocean. ...
