Principles of protein structural ensemble determination
Highlights•The principles of protein structural ensemble determination are described.•The
use of experimental data averaged over multiple states is analysed.•Approaches for …
use of experimental data averaged over multiple states is analysed.•Approaches for …
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference
More than 100,000 protein structures are now known at atomic detail. However, far more are
not yet known, particularly among large or complex proteins. Often, experimental information …
not yet known, particularly among large or complex proteins. Often, experimental information …
Integrative approaches in structural biology: a more complete picture from the combination of individual techniques
With the recent technological and computational advancements, structural biology has
begun to tackle more and more difficult questions, including complex biochemical pathways …
begun to tackle more and more difficult questions, including complex biochemical pathways …
A Bayesian approach to quantifying uncertainty from experimental noise in DEER spectroscopy
TH Edwards, S Stoll - Journal of magnetic resonance, 2016 - Elsevier
Abstract Double Electron-Electron Resonance (DEER) spectroscopy is a solid-state pulse
Electron Paramagnetic Resonance (EPR) experiment that measures distances between …
Electron Paramagnetic Resonance (EPR) experiment that measures distances between …
Blind protein structure prediction using accelerated free-energy simulations
We report a key proof of principle of a new acceleration method [Modeling Employing
Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It …
Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It …
Toward structure prediction of cyclic peptides
Cyclic peptides are a promising class of molecules that can be used to target specific protein–
protein interactions. A computational method to accurately predict their structures would …
protein interactions. A computational method to accurately predict their structures would …
Reconciling simulated ensembles of apomyoglobin with experimental hydrogen/deuterium exchange data using bayesian inference and multiensemble markov state …
Hydrogen/deuterium exchange (HDX) is a powerful technique to investigate protein
conformational dynamics at amino acid resolution. Because HDX provides a measurement …
conformational dynamics at amino acid resolution. Because HDX provides a measurement …
Molecular simulation of conformational pre-organization in cyclic RGD peptides
To test the ability of molecular simulations to accurately predict the solution-state
conformational properties of peptidomimetics, we examined a test set of 18 cyclic RGD …
conformational properties of peptidomimetics, we examined a test set of 18 cyclic RGD …
Insights into peptoid helix folding cooperativity from an improved backbone potential
S Mukherjee, G Zhou, C Michel… - The Journal of Physical …, 2015 - ACS Publications
Peptoids (N-substituted oligoglycines) are biomimetic polymers that can fold into a variety of
unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky …
unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky …
Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeus
Antibiotic resistance is a serious threat to global public health, and methicillin-resistant
Staphylococcus aureus (MRSA) is a poignant example. The macrolactone natural product …
Staphylococcus aureus (MRSA) is a poignant example. The macrolactone natural product …