Daniel A. Keedy
Daniel A. Keedy
CUNY Advanced Science Research Center
Verified email at gc.cuny.edu - Homepage
Cited by
Cited by
MolProbity: all-atom structure validation for macromolecular crystallography
VB Chen, WB Arendall, JJ Headd, DA Keedy, RM Immormino, GJ Kapral, ...
Acta Crystallographica Section D: Biological Crystallography 66 (1), 12-21, 2010
MolProbity: More and better reference data for improved all‐atom structure validation
CJ Williams, JJ Headd, NW Moriarty, MG Prisant, LL Videau, LN Deis, ...
Protein Science 27 (1), 293-315, 2018
Alternate states of proteins revealed by detailed energy landscape mapping
MD Tyka, DA Keedy, I André, F DiMaio, Y Song, DC Richardson, ...
Journal of molecular biology 405 (2), 607-618, 2011
osprey: Protein Design with Ensembles, Flexibility, and Provable Algorithms.
P Gainza, KE Roberts, I Georgiev, RH Lilien, DA Keedy, CY Chen, F Reza, ...
Methods in enzymology 523, 87, 2013
CryptoSite: expanding the druggable proteome by characterization and prediction of cryptic binding sites
P Cimermancic, P Weinkam, TJ Rettenmaier, L Bichmann, DA Keedy, ...
Journal of molecular biology 428 (4), 709-719, 2016
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography
DA Keedy, LR Kenner, M Warkentin, RA Woldeyes, JB Hopkins, ...
Elife 4, e07574, 2015
Dead‐End elimination with perturbations (“DEEPer”): A provable protein design algorithm with continuous sidechain and backbone flexibility
MA Hallen, DA Keedy, BR Donald
Proteins: Structure, Function, and Bioinformatics, 2012
Ultrasonic characterization of human cancellous bone in vitro using three different apparent backscatter parameters in the frequency range 0.6-15.0 MHz
BK Hoffmeister, DP Johnson, JA Janeski, DA Keedy, BW Steinert, ...
IEEE transactions on ultrasonics, ferroelectrics, and frequency control 55 …, 2008
The other 90% of the protein: Assessment beyond the Cαs for CASP8 template‐based and high‐accuracy models
DA Keedy, CJ Williams, JJ Headd, WB Arendall III, VB Chen, GJ Kapral, ...
Proteins: Structure, Function, and Bioinformatics 77 (S9), 29-49, 2009
Algorithm for backrub motions in protein design
I Georgiev, D Keedy, JS Richardson, DC Richardson, BR Donald
Bioinformatics 24 (13), i196-i204, 2008
Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR
DA Keedy, H Van Den Bedem, DA Sivak, GA Petsko, D Ringe, MA Wilson, ...
Structure 22 (6), 899-910, 2014
An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering
DA Keedy, ZB Hill, JT Biel, E Kang, TJ Rettenmaier, J Brandao-Neto, ...
Elife 7, e36307, 2018
Exposing hidden alternative backbone conformations in X-ray crystallography using qFit
DA Keedy, JS Fraser, H Van Den Bedem
PLoS Comput Biol 11 (10), e1004507, 2015
Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place
JJ Headd, RM Immormino, DA Keedy, P Emsley, DC Richardson, ...
Journal of structural and functional genomics 10 (1), 83-93, 2009
Conformational variation of proteins at room temperature is not dominated by radiation damage
S Russi, A González, LR Kenner, DA Keedy, JS Fraser, H Bedem
Journal of synchrotron radiation 24 (1), 73-82, 2017
The role of local backrub motions in evolved and designed mutations
DA Keedy, I Georgiev, EB Triplett, BR Donald, DC Richardson, ...
PLoS Comput Biol 8 (8), e1002629, 2012
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps
GC Van Zundert, BM Hudson, SHP de Oliveira, DA Keedy, R Fonseca, ...
Journal of medicinal chemistry 61 (24), 11183-11198, 2018
“The plot” thickens: more data, more dimensions, more uses
JS Richardson, DA Keedy, DC Richardson
Biomolecular Forms and Functions: A Celebration of 50 Years of the …, 2013
Journey to the center of the protein: Allostery from multitemperature multiconformer X-ray crystallography
DA Keedy
Acta Crystallographica Section D: Structural Biology 75 (2), 123-137, 2019
Orbital motion of electrically charged spheres in microgravity
S Banerjee, K Andring, D Campbell, J Janeski, D Keedy, S Quinn, ...
The Physics Teacher 46 (8), 460-464, 2008
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