Deep learning for computational chemistry

GB Goh, NO Hodas, A Vishnu - Journal of computational …, 2017 - Wiley Online Library
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 …

Mass spectrometry-based protein footprinting for higher-order structure analysis: fundamentals and applications

XR Liu, MM Zhang, ML Gross - Chemical reviews, 2020 - ACS Publications
Proteins adopt different higher-order structures (HOS) to enable their unique biological
functions. Understanding the complexities of protein higher-order structures and dynamics …

Predicting multiple conformations via sequence clustering and AlphaFold2

HK Wayment-Steele, A Ojoawo, R Otten, JM Apitz… - Nature, 2024 - nature.com
Abstract AlphaFold2 (ref.) has revolutionized structural biology by accurately predicting
single structures of proteins. However, a protein's biological function often depends on …

Multistate and functional protein design using RoseTTAFold sequence space diffusion

SL Lisanza, JM Gershon, SWK Tipps, JN Sims… - Nature …, 2024 - nature.com
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 …

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 …

NMRbox: a resource for biomolecular NMR computation

MW Maciejewski, AD Schuyler, MR Gryk, II Moraru… - Biophysical journal, 2017 - cell.com
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 …

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 …

Solid-state NMR: Methods for biological solids

S Ahlawat, KR Mote, NA Lakomek… - Chemical Reviews, 2022 - ACS Publications
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has
transformed from a spectroscopic technique investigating small molecules and industrial …

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 …

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

Y Shen, F Delaglio, G Cornilescu, A Bax - Journal of biomolecular NMR, 2009 - Springer
NMR chemical shifts in proteins depend strongly on local structure. The program TALOS
establishes an empirical relation between 13 C, 15 N and 1 H chemical shifts and backbone …