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 …

Cryo-EM in drug discovery: achievements, limitations and prospects

JP Renaud, A Chari, C Ciferri, W Liu… - Nature reviews Drug …, 2018 - nature.com
Cryo-electron microscopy (cryo-EM) of non-crystalline single particles is a biophysical
technique that can be used to determine the structure of biological macromolecules and …

[HTML][HTML] Structure of Hsp90–Hsp70–Hop–GR reveals the Hsp90 client-loading mechanism

RYR Wang, CM Noddings, E Kirschke, AG Myasnikov… - Nature, 2022 - nature.com
Maintaining a healthy proteome is fundamental for the survival of all organisms. Integral to
this are Hsp90 and Hsp70, molecular chaperones that together facilitate the folding …

[HTML][HTML] Structure of microbial nanowires reveals stacked hemes that transport electrons over micrometers

F Wang, Y Gu, JP O'Brien, MY Sophia, SE Yalcin… - Cell, 2019 - cell.com
Summary Long-range (> 10 μm) transport of electrons along networks of Geobacter
sulfurreducens protein filaments, known as microbial nanowires, has been invoked to …

Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion

AC Walls, MA Tortorici, J Snijder… - Proceedings of the …, 2017 - National Acad Sciences
The tremendous pandemic potential of coronaviruses was demonstrated twice in the past
few decades by two global outbreaks of deadly pneumonia. The coronavirus spike (S) …

Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules

H Park, P Bradley, P Greisen Jr, Y Liu… - Journal of chemical …, 2016 - ACS Publications
Most biomolecular modeling energy functions for structure prediction, sequence design, and
molecular docking have been parametrized using existing macromolecular structural data; …

Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

AC Walls, MA Tortorici, BJ Bosch, B Frenz, PJM Rottier… - Nature, 2016 - nature.com
The tremendous pandemic potential of coronaviruses was demonstrated twice in the past
few decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells …

Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase

KA Verba, RYR Wang, A Arakawa, Y Liu, M Shirouzu… - Science, 2016 - science.org
The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate
more than half of the human kinome. However, both the mechanism by which these …

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

RYR Wang, Y Song, BA Barad, Y Cheng, JS Fraser… - Elife, 2016 - elifesciences.org
Cryo-EM has revealed the structures of many challenging yet exciting macromolecular
assemblies at near-atomic resolution (3–4.5 Å), providing biological phenomena with …

A structural model of the endogenous human BAF complex informs disease mechanisms

N Mashtalir, H Suzuki, DP Farrell, A Sankar, J Luo… - Cell, 2020 - cell.com
Mammalian SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that
regulate genomic architecture. Here, we present a structural model of the endogenously …