Integrative, dynamic structural biology at atomic resolution—it's about time
H Van Den Bedem, JS Fraser - Nature methods, 2015 - nature.com
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to
interact with binding partners or perform the chemical reactions required for a multitude of …
interact with binding partners or perform the chemical reactions required for a multitude of …
Rigidity theory for biomolecules: concepts, software, and applications
SMA Hermans, C Pfleger, C Nutschel… - Wiley …, 2017 - Wiley Online Library
The mechanical heterogeneity of biomolecular structures is intimately linked to their diverse
biological functions. Applying rigidity theory to biomolecules identifies this heterogeneous …
biological functions. Applying rigidity theory to biomolecules identifies this heterogeneous …
Exposing hidden alternative backbone conformations in X-ray crystallography using qFit
Proteins must move between different conformations of their native ensemble to perform
their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect …
their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect …
[图书][B] Modeling structure and dynamics of protein complexes with SAXS profiles
D Schneidman-Duhovny, M Hammel - 2018 - Springer
Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for
structural characterization of molecules in solution. A SAXS experiment determines the …
structural characterization of molecules in solution. A SAXS experiment determines the …
Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids
B Liu, H Shi, HM Al-Hashimi - Current opinion in structural biology, 2021 - Elsevier
Nucleic acids do not fold into a single conformation, and dynamic ensembles are needed to
describe their propensities to cycle between different conformations when performing …
describe their propensities to cycle between different conformations when performing …
Shortening the HIV-1 TAR RNA bulge by a single nucleotide preserves motional modes over a broad range of time scales
Helix–junction–helix (HJH) motifs are flexible building blocks of RNA architecture that help
define the orientation and dynamics of helical domains. They are also frequently involved in …
define the orientation and dynamics of helical domains. They are also frequently involved in …
Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities
A Guilhot-Gaudeffroy, C Froidevaux, J Azé, J Bernauer - PloS one, 2014 - journals.plos.org
Protein-RNA complexes provide a wide range of essential functions in the cell. Their atomic
experimental structure solving, despite essential to the understanding of these functions, is …
experimental structure solving, despite essential to the understanding of these functions, is …
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations
D Budday, S Leyendecker, H van den Bedem - Journal of the Mechanics …, 2015 - Elsevier
Proteins operate and interact with partners by dynamically exchanging between functional
substates of a conformational ensemble on a rugged free energy landscape. Understanding …
substates of a conformational ensemble on a rugged free energy landscape. Understanding …
Role of conformational heterogeneity in ligand recognition by viral RNA molecules
L Levintov, H Vashisth - Physical Chemistry Chemical Physics, 2021 - pubs.rsc.org
Ribonucleic acid (RNA) molecules are known to undergo conformational changes in
response to various environmental stimuli including temperature, pH, and ligands. In …
response to various environmental stimuli including temperature, pH, and ligands. In …
GARN: Sampling RNA 3D structure space with game theory and knowledge-based scoring strategies
Cellular processes involve large numbers of RNA molecules. The functions of these RNA
molecules and their binding to molecular machines are highly dependent on their 3D …
molecules and their binding to molecular machines are highly dependent on their 3D …