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Two-component signal transduction in Bacillus subtilis: how one organism sees its world.
Variability and adaptability are crucial characteristics of organisms possessing the ability to survive and prosper in a wide variety of environmental conditions. The most adaptable bacteria containExpand
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Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that followsExpand
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Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator AbrB
We have determined the high resolution NMR solution structure of the novel DNA binding domain of the Bacillus subtilis transition state regulator AbrB. Comparisons of the AbrB DNA binding domain withExpand
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Emerging Computational Methods for the Rational Discovery of Allosteric Drugs
Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date, the discovery of allosteric binding sitesExpand
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D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (1) HSP90,Expand
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Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions.
Several variants of T4 lysozyme have been identified that sequester small organic ligands in cavities or clefts. To evaluate potential binding sites for non-polar molecules, we screened a number ofExpand
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Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F
Protein backbones and side chains display varying degrees of flexibility, which allows many slightly different but related conformational substates to occur. Such fluctuations are known to differ inExpand
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Access of ligands to cavities within the core of a protein is rapid
We have investigated the magnitude and timescale of fluctuations within the core of a protein using the exchange kinetics of indole and benzene binding to engineered hydrophobic cavities in T4Expand
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Computational approaches to mapping allosteric pathways.
Allosteric signaling occurs when chemical and/or physical changes at an allosteric site alter the activity of a primary orthosteric site often many Ångströms distant. A number of recently developedExpand
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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomicExpand
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