[PDF][PDF] Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

D Liebschner, PV Afonine, ML Baker… - … Section D: Structural …, 2019 - journals.iucr.org
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods
to determine three-dimensional macromolecular structures, which are required to …

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Structure of the bacterial ribosome at 2 Å resolution

ZL Watson, FR Ward, R Méheust, O Ad, A Schepartz… - elife, 2020 - elifesciences.org
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia
coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous …

Structure, folding and flexibility of co-transcriptional RNA origami

EKS McRae, HØ Rasmussen, J Liu, A Bøggild… - Nature …, 2023 - nature.com
RNA origami is a method for designing RNA nanostructures that can self-assemble through
co-transcriptional folding with applications in nanomedicine and synthetic biology. However …

MolProbity: more and better reference data for improved all‐atom structure validation

CJ Williams, JJ Headd, NW Moriarty… - Protein …, 2018 - Wiley Online Library
This paper describes the current update on macromolecular model validation services that
are provided at the MolProbity website, emphasizing changes and additions since the …

FARFAR2: improved de novo rosetta prediction of complex global RNA folds

AM Watkins, R Rangan, R Das - Structure, 2020 - cell.com
Predicting RNA three-dimensional structures from sequence could accelerate
understanding of the growing number of RNA molecules being discovered across biology …

[PDF][PDF] MolProbity: all-atom structure validation for macromolecular crystallography

VB Chen, WB Arendall, JJ Headd… - … Section D: Biological …, 2010 - journals.iucr.org
MolProbity is a structure-validation web service that provides broad-spectrum solidly based
evaluation of model quality at both the global and local levels for both proteins and nucleic …

The Phenix software for automated determination of macromolecular structures

PD Adams, PV Afonine, G Bunkóczi, VB Chen… - Methods, 2011 - Elsevier
X-ray crystallography is a critical tool in the study of biological systems. It is able to provide
information that has been a prerequisite to understanding the fundamentals of life. It is also a …

[PDF][PDF] PHENIX: a comprehensive Python-based system for macromolecular structure solution

PD Adams, PV Afonine, G Bunkóczi… - … Section D: Biological …, 2010 - journals.iucr.org
Macromolecular X-ray crystallography is routinely applied to understand biological
processes at a molecular level. However, significant time and effort are still required to solve …

Impact of 2′‐hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all‐atom additive force field for RNA

EJ Denning, UD Priyakumar, L Nilsson… - Journal of …, 2011 - Wiley Online Library
Here, we present an update of the CHARMM27 all‐atom additive force field for nucleic acids
that improves the treatment of RNA molecules. The original CHARMM27 force field …