[HTML][HTML] A practical guide to large-scale docking

BJ Bender, S Gahbauer, A Luttens, J Lyu, CM Webb… - Nature protocols, 2021 - nature.com
Abstract Structure-based docking screens of large compound libraries have become
common in early drug and probe discovery. As computer efficiency has improved and …

Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors

T Patriarchi, JR Cho, K Merten, MW Howe, A Marley… - Science, 2018 - science.org
INTRODUCTION Neuromodulators, such as dopamine, norepinephrine, or serotonin, exert
powerful control over neural circuit dynamics that give rise to diverse neural function and …

An expanded palette of dopamine sensors for multiplex imaging in vivo

T Patriarchi, A Mohebi, J Sun, A Marley, R Liang… - Nature …, 2020 - nature.com
Genetically encoded dopamine sensors based on green fluorescent protein (GFP) enable
high-resolution imaging of dopamine dynamics in behaving animals. However, these GFP …

[HTML][HTML] Cryo-electron microscopy for structural analysis of dynamic biological macromolecules

K Murata, M Wolf - Biochimica et Biophysica Acta (BBA)-General Subjects, 2018 - Elsevier
Background Since the introduction of what became today's standard for cryo-embedding of
biological macromolecules at native conditions more than 30 years ago, techniques and …

Hierarchical materials from high information content macromolecular building blocks: construction, dynamic interventions, and prediction

L Shao, J Ma, JL Prelesnik, Y Zhou, M Nguyen… - Chemical …, 2022 - ACS Publications
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature.
Because hierarchy gives rise to unique properties and functions, many have sought …

De novo metalloprotein design

MJ Chalkley, SI Mann, WF DeGrado - Nature Reviews Chemistry, 2022 - nature.com
Natural metalloproteins perform many functions—ranging from sensing to electron transfer
and catalysis—in which the position and property of each ligand and metal are dictated by …

[HTML][HTML] Directed evolution of a selective and sensitive serotonin sensor via machine learning

EK Unger, JP Keller, M Altermatt, R Liang, A Matsui… - Cell, 2020 - cell.com
Serotonin plays a central role in cognition and is the target of most pharmaceuticals for
psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will …

[HTML][HTML] Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

JG Greener, SM Kandathil, DT Jones - Nature communications, 2019 - nature.com
The inapplicability of amino acid covariation methods to small protein families has limited
their use for structural annotation of whole genomes. Recently, deep learning has shown …

[HTML][HTML] Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

B Li, YT Yang, JA Capra… - PLoS computational …, 2020 - journals.plos.org
Predicting mutation-induced changes in protein thermodynamic stability (ΔΔG) is of great
interest in protein engineering, variant interpretation, and protein biophysics. We introduce …