The Bio3D packages for structural bioinformatics
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and
dynamics. Major functionality includes biomolecular database searching and retrieval …
dynamics. Major functionality includes biomolecular database searching and retrieval …
Advances in NMR methods to map allosteric sites: from models to translation
The last five years have witnessed major developments in the understanding of the allosteric
phenomenon, broadly defined as coupling between remote molecular sites. Such advances …
phenomenon, broadly defined as coupling between remote molecular sites. Such advances …
Integrating protein structural dynamics and evolutionary analysis with Bio3D
Background Popular bioinformatics approaches for studying protein functional dynamics
include comparisons of crystallographic structures, molecular dynamics simulations and …
include comparisons of crystallographic structures, molecular dynamics simulations and …
Modeling coronavirus spike protein dynamics: implications for immunogenicity and immune escape
The ongoing COVID-19 pandemic is a global public health emergency requiring urgent
development of efficacious vaccines. While concentrated research efforts have focused …
development of efficacious vaccines. While concentrated research efforts have focused …
Identification of high-affinity pyridoxal kinase inhibitors targeting cancer therapy: an integrated docking and molecular dynamics simulation approach
Pyridoxal kinase (PDXK) is a vitamin B6-dependent transferase enzyme encoded by the
PDXK gene, crucial for leukemic cell proliferation. Disruption of its activity causes altered …
PDXK gene, crucial for leukemic cell proliferation. Disruption of its activity causes altered …
NMR spectroscopy on domain dynamics in biomacromolecules
YE Shapiro - Progress in Biophysics and Molecular Biology, 2013 - Elsevier
Abstract Domain dynamics in biomacromolecules is currently an area of intense research
because of its importance for understanding the huge quantity of available data relating the …
because of its importance for understanding the huge quantity of available data relating the …
[HTML][HTML] SPECTRUS: A dimensionality reduction approach for identifying dynamical domains in protein complexes from limited structural datasets
Identifying dynamical, quasi-rigid domains in proteins provides a powerful means for
characterizing functionally oriented structural changes via a parsimonious set of degrees of …
characterizing functionally oriented structural changes via a parsimonious set of degrees of …
Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes
Aminoglycoside antibiotics are used against severe bacterial infections. They bind to the
bacterial ribosomal RNA and interfere with the translation process. However, bacteria …
bacterial ribosomal RNA and interfere with the translation process. However, bacteria …
[HTML][HTML] Structural plasticity of arrestin-G protein coupled receptor complexes as a molecular determinant of signaling
G protein coupled receptors (GPCRs) are critically regulated by arrestins. In this study, high-
resolution data was combined with molecular dynamics simulations to infer the determinants …
resolution data was combined with molecular dynamics simulations to infer the determinants …
“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations
Characterizing a protein mutational landscape is a very challenging problem in Biology.
Many disease-associated mutations do not seem to produce any effect on the global shape …
Many disease-associated mutations do not seem to produce any effect on the global shape …