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Daniel A. Keedy
Daniel A. Keedy
CUNY Advanced Science Research Center
Verified email at gc.cuny.edu - Homepage
Title
Cited by
Cited by
Year
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
140952010
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
29882018
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
3612011
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
1912016
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
1712015
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
1412013
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
1392018
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
1362014
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
1062012
Algorithm for backrub motions in protein design
I Georgiev, D Keedy, JS Richardson, DC Richardson, BR Donald
Bioinformatics 24 (13), i196-i204, 2008
1002008
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
982008
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
972009
Exposing hidden alternative backbone conformations in X-ray crystallography using qFit
DA Keedy, JS Fraser, H van den Bedem
PLoS computational biology 11 (10), e1004507, 2015
892015
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
612017
W., Richardson, JS, and Richardson, DC (2010)." MolProbity: all-atom structure validation for macromolecular crystallography
VB Chen, WB Arendall III, JJ Headd, DA Keedy, RM Immormino, ...
Acta Cryst. D 66, 12-21, 0
51
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps
GCP van Zundert, BM Hudson, SHP de Oliveira, DA Keedy, R Fonseca, ...
Journal of medicinal chemistry 61 (24), 11183-11198, 2018
472018
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, 83-93, 2009
462009
qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps
BT Riley, SA Wankowicz, SHP de Oliveira, GCP van Zundert, DW Hogan, ...
Protein Science 30 (1), 270-285, 2021
352021
The role of local backrub motions in evolved and designed mutations
DA Keedy, I Georgiev, EB Triplett, BR Donald, DC Richardson, ...
Public Library of Science 8 (8), e1002629, 2012
322012
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
312019
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