D. Keedy

发表

Correspondence e-mail:

Vincent B. Chen, Gary J. Kapral, W. B. Arendall, 2000 .

Alternate states of proteins revealed by detailed energy landscape mapping.

D. Baker, F. Dimaio, M. Tyka, 2011, Journal of molecular biology.

“THE PLOT” THICKENS: MORE DATA, MORE DIMENSIONS, MORE USES

J. Richardson, D. Richardson, D. Keedy, 2013 .

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering

Frank von Delft, James S Fraser, Daniel A Keedy, 2018, eLife.

New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering

J. Wells, F. von Delft, J. Fraser, 2017, bioRxiv.

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.

Julie C. Mitchell, Andrej Sali, Dina Schneidman-Duhovny, 2016, Journal of molecular biology.

Mapping the Conformational Landscape of a Dynamic Enzyme by Multitemperature and XFEL Crystallography

Nicholas K. Sauter, Aaron S. Brewster, Jesse B. Hopkins, 2015 .

Figures and figure supplements Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

Jesse B. Hopkins, Andrew H. Van Benschoten, J. Holton, 2016 .

Ultrasonic characterization of human cancellous bone in vitro using three different apparent backscatter parameters in the frequency range 0.6-15.0 mhz

D. Keedy, S. Kaste, B. Hoffmeister, 2008, IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control.

Objectively and automatically building multi-conformer ligand models in electron densities

H. V. D. Bedem, T. Day, K. Borrelli, 2017 .

Using Protein-Likeness to Validate Conformational Alternatives

D. Keedy, 2012 .

Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

J. Fraser, D. Keedy, H. van den Bedem, 2015, bioRxiv.

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.

H. V. D. Bedem, T. Day, K. Borrelli, 2018 .

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

T. Day, K. Borrelli, A. Héliou, 2018, bioRxiv.

Dead‐end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility

Mark A Hallen, B. Donald, D. Keedy, 2013, Proteins.

Use of a Tensile Testing Machine for the Determination of Stress and Strain‐Optical Coefficients

D. Keedy, H. Kawai, Richard J. Volungis, 1961 .

Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.

David A Sivak, Henry van den Bedem, David A. Sivak, 2014, Structure.

Room-temperature serial synchrotron crystallography of apo PTP1B

D. Keedy, A. Ebrahim, Shivani Sharma, 2022, bioRxiv.

Multiconformer synchrotron model of CypA at 260 K

H. V. D. Bedem, J. Holton, W. Weis, 2015 .

Multiconformer synchrotron model of CypA at 100 K

H. V. D. Bedem, J. Holton, W. Weis, 2015 .

Multiconformer fixed-target X-ray free electron (XFEL) model of CypA at 273 K

H. V. D. Bedem, J. Holton, W. Weis, 2015 .

High-resolution multiconformer synchrotron model of CypA at 273 K

H. V. D. Bedem, J. Holton, W. Weis, 2015 .

Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B

F. von Delft, D. Keedy, J. Biel, 2022, bioRxiv.

Dynamic light scattering of polyethylene. I. Introduction and experimental procedures

D. Keedy, R. Prud’homme, R. Stein, 1973 .

Dynamic X‐Ray Diffractometer for Measuring Rheo‐Optical Behavior of Crystals in Polymer Solids

D. Keedy, H. Kawai, R. Stein, 1968 .

Dynamic X-Ray Diffraction from Polyethylene

D. Keedy, H. Kawai, R. Stein, 1968 .

Depolarization of Scattered Light by n‐Paraffin Vapors and the Additivity of Bond Polarizability Tensors

D. Keedy, R. Stein, J. Powers, 1961 .

A Theoretical Calculation of the Briefringence of Polypropylene Crystals

D. Keedy, R. Stein, J. Powers, 1960 .

MolProbity: More and better reference data for improved all‐atom structure validation

Christopher J. Williams, Jack Snoeyink, Vishal Verma, 2018, Protein science : a publication of the Protein Society.

Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography

D. Keedy, 2019, Acta crystallographica. Section D, Structural biology.

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)

D. Keedy, A. Ebrahim, D. Kumaran, 2022, IUCrJ.

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)

D. Keedy, A. Ebrahim, S. McSweeney, 2021, bioRxiv.

The Role of Local Backrub Motions in Evolved and Designed Mutations

Bruce Randall Donald, Ivelin Georgiev, David C. Richardson, 2012, PLoS Comput. Biol..

Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields

Vincent A. Voelz, D. Mobley, M. Wall, 2023, 2303.11056.

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place

Jeffrey J. Headd, David C. Richardson, Paul Emsley, 2008, Journal of Structural and Functional Genomics.

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

Henry van den Bedem, James S. Fraser, Daniel A. Keedy, 2015, bioRxiv.

Osprey: Protein Design with Ensembles, Flexibility, and Provable Algorithms

Pablo Gainza, Ivelin Georgiev, Cheng-Yu Chen, 2022 .

The dynamic birefringence of high polymers

D. Keedy, S. Onogi, R. Stein, 1962 .

Ultrastructures of rabbit corneal stroma: mapping of optical and morphological anisotropies.

D. Keedy, J. Chien, E. Chang, 1974, Biochimica et biophysica acta.

qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps

Saulo H. P. de Oliveira, J. Fraser, D. Keedy, 2020, Protein science : a publication of the Protein Society.

qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps

Henry van den Bedem, Blake T. Riley, Gydo C. P. van Zundert, 2020, bioRxiv.

qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.

Henry van den Bedem, Pooja Suresh, Rasmus Fonseca, 2018, Journal of medicinal chemistry.

Model Selection for Biological Crystallography

Nathan S. Babcock, David A. Sivak, James S. Fraser, 2018, bioRxiv.

Exposing hidden alternative backbone conformations 1 in X-ray crystallography using qFit 2 3

H. V. D. Bedem, J. Fraser, D. Keedy, 2015 .

Dynamic Birefringence of High Polymers II

D. Keedy, S. Onogi, R. Stein, 1963 .

Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase

D. Keedy, A. Ebrahim, B. Riley, 2023, bioRxiv.

The measurement of the orientation rate of crystals in a crystalline polymer by dynamic x-ray diffraction

D. Keedy, R. Stein, T. Itoh, 1964 .

The measurement of dynamic birefringence

D. Keedy, S. Onogi, R. Stein, 1961 .

Conformational variation of proteins at room temperature is not dominated by radiation damage

Henry van den Bedem, James S. Fraser, Daniel A. Keedy, 2017, Journal of synchrotron radiation.

Algorithm for backrub motions in protein design

Bruce Randall Donald, Ivelin Georgiev, David C. Richardson, 2008, ISMB.

The other 90% of the protein: Assessment beyond the Cαs for CASP8 template‐based and high‐accuracy models

Christopher J. Williams, Adam Zemla, Vincent B. Chen, 2009, Proteins.

assessment Authors:

Christopher J. Williams, Vincent B. Chen, Jeremy N. Block, 2009 .

Native dynamics and allosteric responses in PTP1B probed by high-resolution HDX-MS

D. Keedy, R. Abzalimov, Virgil A. Woods, 2023, bioRxiv.

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen, Gary J. Kapral, W. B. Arendall, 2009, Acta crystallographica. Section D, Biological crystallography.

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

J. Fraser, D. Keedy, H. van den Bedem, 2023, bioRxiv.

High-resolution double vision of the archetypal protein tyrosine phosphatase

D. Keedy, Tamar (Skaist) Mehlman, R. Sagabala, 2023, bioRxiv.

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen, Jeffrey J. Headd, David C. Richardson, 2009, Acta crystallographica. Section D, Biological crystallography.

The other 90% of the protein: Assessment beyond the Cαs for CASP8 template‐based and high‐accuracy models

Christopher J. Williams, Vincent B. Chen, Jeremy N. Block, 2009, Proteins.

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

Andrew H. Van Benschoten, H. V. D. Bedem, A. Brunger, 2015, bioRxiv.

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen, Gary J. Kapral, W. B. Arendall, 2009, Acta crystallographica. Section D, Biological crystallography.

OSPREY: protein design with ensembles, flexibility, and provable algorithms.

Kyle E. Roberts, J. Richardson, R. Lilien, 2013, Methods in enzymology.

Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP

D. Keedy, B. Riley, Liliana Guerrero, 2024, Communications biology.

An expanded trove of fragment-bound structures for the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data

D. Keedy, T. Mehlman, Helen M. Ginn, 2024, Structure.

An expanded view of ligandability in the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data

D. Keedy, Helen M. Ginn, Tamar (Skaist) Mehlman, 2024, bioRxiv.

AI is a viable alternative to high throughput screening: a 318-target study

Eva M García-Cuesta, Frederick S. Vizeacoumar, Stephen J. Capuzzi, 2024, Scientific reports.

Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction

Neel H. Shah, D. Keedy, Yunyao Xu, 2024, bioRxiv.