User profiles for D. A. Keedy
Daniel A. KeedyCUNY Advanced Science Research Center Verified email at gc.cuny.edu Cited by 18813 |
[HTML][HTML] MolProbity: all-atom structure validation for macromolecular crystallography
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 …
evaluation of model quality at both the global and local levels for both proteins and nucleic …
MolProbity: More and better reference data for improved all‐atom structure validation
This paper describes the current update on macromolecular model validation services that
are provided at the MolProbity website, emphasizing changes and additions since the …
are provided at the MolProbity website, emphasizing changes and additions since the …
Alternate states of proteins revealed by detailed energy landscape mapping
What conformations do protein molecules populate in solution? Crystallography provides a
high-resolution description of protein structure in the crystal environment, while NMR …
high-resolution description of protein structure in the crystal environment, while NMR …
CryptoSite: expanding the druggable proteome by characterization and prediction of cryptic binding sites
Many proteins have small-molecule binding pockets that are not easily detectable in the
ligand-free structures. These cryptic sites require a conformational change to become apparent; …
ligand-free structures. These cryptic sites require a conformational change to become apparent; …
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography
10.7554/eLife.07574.001 Determining the interconverting conformations of dynamic proteins
in atomic detail is a major challenge for structural biology. Conformational heterogeneity in …
in atomic detail is a major challenge for structural biology. Conformational heterogeneity in …
[PDF][PDF] Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR
Most macromolecular X-ray structures are determined from cryocooled crystals, but it is
unclear whether cryocooling distorts functionally relevant flexibility. Here we compare …
unclear whether cryocooling distorts functionally relevant flexibility. Here we compare …
An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering
10.7554/eLife.36307.001 Allostery is an inherent feature of proteins, but it remains challenging
to reveal the mechanisms by which allosteric signals propagate. A clearer understanding …
to reveal the mechanisms by which allosteric signals propagate. A clearer understanding …
OSPREY: protein design with ensembles, flexibility, and provable algorithms
We have developed a suite of protein redesign algorithms that improves realistic in silico
modeling of proteins. These algorithms are based on three characteristics that make them …
modeling of proteins. These algorithms are based on three characteristics that make them …
Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B
Much of our current understanding of how small-molecule ligands interact with proteins stems
from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone…
from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone…
Dead‐end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility
Computational protein and drug design generally require accurate modeling of protein
conformations. This modeling typically starts with an experimentally determined protein structure …
conformations. This modeling typically starts with an experimentally determined protein structure …