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

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 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. Williams CJ, et al. Among authors: keedy da. Protein Sci. 2018 Jan;27(1):293-315. doi: 10.1002/pro.3330. Epub 2017 Nov 27. Protein Sci. 2018. PMID: 29067766 Free PMC article.

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MolProbity: all-atom structure validation for macromolecular crystallography.

Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. Chen VB, et al. Among authors: keedy da. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21. doi: 10.1107/S0907444909042073. Epub 2009 Dec 21. Acta Crystallogr D Biol Crystallogr. 2010. PMID: 20057044 Free PMC article.

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

Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H. Riley BT, et al. Among authors: keedy da. Protein Sci. 2021 Jan;30(1):270-285. doi: 10.1002/pro.4001. Epub 2020 Nov 30. Protein Sci. 2021. PMID: 33210433 Free PMC article.

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The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M^pro).

Ebrahim A, Riley BT, Kumaran D, Andi B, Fuchs MR, McSweeney S, Keedy DA. Ebrahim A, et al. Among authors: keedy da. bioRxiv. 2021 Nov 7:2021.05.03.437411. doi: 10.1101/2021.05.03.437411. Preprint. bioRxiv. 2021. PMID: 33972941 Free PMC article.

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

Keedy DA. Keedy DA. Acta Crystallogr D Struct Biol. 2019 Feb 1;75(Pt 2):123-137. doi: 10.1107/S2059798318017941. Epub 2019 Jan 28. Acta Crystallogr D Struct Biol. 2019. PMID: 30821702 Free PMC article.

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

Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. Keedy DA, et al. Elife. 2018 Jun 7;7:e36307. doi: 10.7554/eLife.36307. Elife. 2018. PMID: 29877794 Free PMC article.

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

van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H. van Zundert GCP, et al. Among authors: keedy da. J Med Chem. 2018 Dec 27;61(24):11183-11198. doi: 10.1021/acs.jmedchem.8b01292. Epub 2018 Dec 6. J Med Chem. 2018. PMID: 30457858 Free PMC article.

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

Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H. Russi S, et al. Among authors: keedy da. J Synchrotron Radiat. 2017 Jan 1;24(Pt 1):73-82. doi: 10.1107/S1600577516017343. Epub 2017 Jan 1. J Synchrotron Radiat. 2017. PMID: 28009548 Free PMC article.

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

Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. Gainza P, et al. Among authors: keedy da. Methods Enzymol. 2013;523:87-107. doi: 10.1016/B978-0-12-394292-0.00005-9. Methods Enzymol. 2013. PMID: 23422427 Free PMC article.

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

Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. Cimermancic P, et al. Among authors: keedy da. J Mol Biol. 2016 Feb 22;428(4):709-719. doi: 10.1016/j.jmb.2016.01.029. Epub 2016 Feb 5. J Mol Biol. 2016. PMID: 26854760 Free PMC article.

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