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 …

Using PyMOL as a platform for computational drug design

S Yuan, HCS Chan, Z Hu - Wiley Interdisciplinary Reviews …, 2017 - Wiley Online Library
PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐
dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron …

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)

S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew… - PloS one, 2013 - journals.plos.org
The Rosetta molecular modeling software package provides experimentally tested and
rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins …

[PDF][PDF] Precise in vivo RNA base editing with a wobble-enhanced circular CLUSTER guide RNA

P Reautschnig, C Fruhner, N Wahn, CP Wiegand… - Nature …, 2024 - nature.com
Recruiting the endogenous editing enzyme adenosine deaminase acting on RNA (ADAR)
with tailored guide RNAs for adenosine-to-inosine (A-to-I) RNA base editing is promising for …

Benchmarking and analysis of protein docking performance in Rosetta v3. 2

S Chaudhury, M Berrondo, BD Weitzner, P Muthu… - PloS one, 2011 - journals.plos.org
RosettaDock has been increasingly used in protein docking and design strategies in order
to predict the structure of protein-protein interfaces. Here we test capabilities of RosettaDock …

Protocols for molecular modeling with Rosetta3 and RosettaScripts

BJ Bender, A Cisneros III, AM Duran, JA Finn, D Fu… - Biochemistry, 2016 - ACS Publications
Previously, we published an article providing an overview of the Rosetta suite of
biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, KW …

An integrated framework advancing membrane protein modeling and design

RF Alford, J Koehler Leman, BD Weitzner… - PLoS computational …, 2015 - journals.plos.org
Membrane proteins are critical functional molecules in the human body, constituting more
than 30% of open reading frames in the human genome. Unfortunately, a myriad of …

Network Pharmacology‐Based and Molecular Docking‐Based Analysis of Suanzaoren Decoction for the Treatment of Parkinson's Disease with Sleep Disorder

Y Liu, L Yu, J Zhang, D Xie, X Zhang… - BioMed research …, 2021 - Wiley Online Library
This study is aimed at exploring the possible mechanism of action of the Suanzaoren
decoction (SZRD) in the treatment of Parkinson's disease with sleep disorder (PDSD) based …

Emerging role of rare earth elements in biomolecular functions

W Yang, K Wu, H Chen, J Huang, Z Yu - The ISME Journal, 2024 - academic.oup.com
The importance of rare earth elements is increasingly recognized due to the increased
demand for their mining and separation. This demand is driving research on the biology of …

Jianpi Huayu Decoction suppresses cellular senescence in colorectal cancer via p53-p21-Rb pathway: Network pharmacology and in vivo validation

S Wang, Y Xing, R Wang, Z Jin - Journal of Ethnopharmacology, 2024 - Elsevier
Abstract Ethnopharmacological relevance Jianpi Huayu Decoction (JHD) is an herbal
prescription in traditional Chinese medicine based on Sijunzi Decoction to treat patients with …