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Daniel A. Keedy, Ph.D. - Publications

Affiliations: 
2012 Biochemistry Duke University, Durham, NC 
Area:
3D structures of proteins
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26 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Mehlman TS, Ginn HM, Keedy DA. An expanded view of ligandability in the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data. Biorxiv : the Preprint Server For Biology. PMID 38260327 DOI: 10.1101/2024.01.05.574428  0.322
2024 Sharma S, Skaist Mehlman T, Sagabala RS, Boivin B, Keedy DA. High-resolution double vision of the allosteric phosphatase PTP1B. Acta Crystallographica. Section F, Structural Biology Communications. 80: 1-12. PMID 38133579 DOI: 10.1107/S2053230X23010749  0.388
2023 Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Hogan DW, van den Bedem H, Keedy DA, Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. Biorxiv : the Preprint Server For Biology. PMID 37425870 DOI: 10.1101/2023.06.28.546963  0.456
2023 Sharma S, Ebrahim A, Keedy DA. Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B. Acta Crystallographica. Section F, Structural Biology Communications. 79: 23-30. PMID 36598353 DOI: 10.1107/S2053230X22011645  0.327
2020 Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H. qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Protein Science : a Publication of the Protein Society. PMID 33210433 DOI: 10.1002/pro.4001  0.368
2019 Keedy DA. Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography. Acta Crystallographica. Section D, Structural Biology. 75: 123-137. PMID 30821702 DOI: 10.1107/S2059798318017941  0.463
2018 van Zundert G, Hudson BM, de Oliveira S, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser J, van den Bedem H. qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps. Journal of Medicinal Chemistry. PMID 30457858 DOI: 10.2210/Pdb6Dmj/Pdb  0.439
2018 Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandao-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. Elife. 7. PMID 29877794 DOI: 10.7554/Elife.36307  0.443
2017 Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB, Snoeyink J, Adams PD, et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Science : a Publication of the Protein Society. PMID 29067766 DOI: 10.1002/Pro.3330  0.64
2017 Babcock NS, Sivak DA, Keedy D, Fraser JS. Model Comparison to Identify Structural Heterogeneity in Protein X-Ray Crystallography Biophysical Journal. 112: 486a. DOI: 10.1016/J.Bpj.2016.11.2628  0.45
2016 Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidmann D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. Journal of Molecular Biology. PMID 26854760 DOI: 10.1016/J.Jmb.2016.01.029  0.413
2015 Keedy DA, Fraser JS, van den Bedem H. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. Plos Computational Biology. 11: e1004507. PMID 26506617 DOI: 10.1371/Journal.Pcbi.1004507  0.476
2015 Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, et al. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife. 4. PMID 26422513 DOI: 10.7554/Elife.07574  0.416
2015 Keedy DA. Conformational and connotational heterogeneity: a surprising relationship between protein structural flexibility and puns. Proteins. 83: 797-8. PMID 25619796 DOI: 10.1002/Prot.24765  0.405
2014 Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Structure (London, England : 1993). 22: 899-910. PMID 24882744 DOI: 10.1016/J.Str.2014.04.016  0.403
2014 Keedy D, van den Bedem H, Rettenmaier J, Wells J, Fraser J. Discovering and Manipulating Protein Conformational Heterogeneity and Function Biophysical Journal. 106: 635a-636a. DOI: 10.1016/J.Bpj.2013.11.3515  0.439
2013 Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods in Enzymology. 523: 87-107. PMID 23422427 DOI: 10.1016/B978-0-12-394292-0.00005-9  0.588
2013 Hallen MA, Keedy DA, Donald BR. Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins. 81: 18-39. PMID 22821798 DOI: 10.1002/Prot.24150  0.483
2013 Hintze BJ, Keedy DA, Richardson DC, Richardson JS. Real Rotamers using Real-Space Correlation Coefficients Biophysical Journal. 104: 547a. DOI: 10.1016/J.Bpj.2012.11.3032  0.576
2012 Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS. The role of local backrub motions in evolved and designed mutations. Plos Computational Biology. 8: e1002629. PMID 22876172 DOI: 10.1371/Journal.Pcbi.1002629  0.64
2012 Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. Chapter 21.6 MolProbity: all-atom structure validation for macromolecular crystallography International Tables For Crystallography. DOI: 10.1107/97809553602060000884  0.747
2011 Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Alternate states of proteins revealed by detailed energy landscape mapping. Journal of Molecular Biology. 405: 607-18. PMID 21073878 DOI: 10.1016/J.Jmb.2010.11.008  0.61
2010 Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography. 66: 12-21. PMID 20057044 DOI: 10.1107/S0907444909042073  0.672
2009 Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS. The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. Proteins. 77: 29-49. PMID 19731372 DOI: 10.1002/Prot.22551  0.594
2009 Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS. Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. Journal of Structural and Functional Genomics. 10: 83-93. PMID 19002604 DOI: 10.1007/S10969-008-9045-8  0.622
2008 Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR. Algorithm for backrub motions in protein design. Bioinformatics (Oxford, England). 24: i196-204. PMID 18586714 DOI: 10.1093/bioinformatics/btn169  0.536
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