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Deep learning for computational chemistry
The rise and fall of artificial neural networks is well documented in the scientific literature of
both computer science and computational chemistry. Yet almost two decades later, we are …
both computer science and computational chemistry. Yet almost two decades later, we are …
Mass spectrometry-based protein footprinting for higher-order structure analysis: fundamentals and applications
Proteins adopt different higher-order structures (HOS) to enable their unique biological
functions. Understanding the complexities of protein higher-order structures and dynamics …
functions. Understanding the complexities of protein higher-order structures and dynamics …
Predicting multiple conformations via sequence clustering and AlphaFold2
Abstract AlphaFold2 (ref.) has revolutionized structural biology by accurately predicting
single structures of proteins. However, a protein's biological function often depends on …
single structures of proteins. However, a protein's biological function often depends on …
Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning
While AlphaFold2 can predict accurate protein structures from the primary sequence,
challenges remain for proteins that undergo conformational changes or for which few …
challenges remain for proteins that undergo conformational changes or for which few …
Multistate and functional protein design using RoseTTAFold sequence space diffusion
Protein denoising diffusion probabilistic models are used for the de novo generation of
protein backbones but are limited in their ability to guide generation of proteins with …
protein backbones but are limited in their ability to guide generation of proteins with …
NMRbox: a resource for biomolecular NMR computation
Advances in computation have been enabling many recent advances in biomolecular
applications of NMR. Due to the wide diversity of applications of NMR, the number and …
applications of NMR. Due to the wide diversity of applications of NMR, the number and …
HSP40 proteins use class-specific regulation to drive HSP70 functional diversity
O Faust, M Abayev-Avraham, AS Wentink, M Maurer… - Nature, 2020 - nature.com
The ubiquitous heat shock protein 70 (HSP70) family consists of ATP-dependent molecular
chaperones, which perform numerous cellular functions that affect almost all aspects of the …
chaperones, which perform numerous cellular functions that affect almost all aspects of the …
Solid-state NMR: Methods for biological solids
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has
transformed from a spectroscopic technique investigating small molecules and industrial …
transformed from a spectroscopic technique investigating small molecules and industrial …
Using chemical shift perturbation to characterise ligand binding
MP Williamson - Progress in nuclear magnetic resonance spectroscopy, 2013 - Elsevier
Chemical shift perturbation (CSP, chemical shift map** or complexation-induced changes
in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is …
in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is …
Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch
A Bah, RM Vernon, Z Siddiqui, M Krzeminski… - Nature, 2015 - nature.com
Intrinsically disordered proteins play important roles in cell signalling, transcription,
translation and cell cycle regulation,. Although they lack stable tertiary structure, many …
translation and cell cycle regulation,. Although they lack stable tertiary structure, many …