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

von Keedy, Daniel A.
Veröffentlicht in Acta Crystallogr D Struct Biol (2019)

Dead-End Elimination with Perturbations (“DEEPer”): A provable protein design algorithm with continuous sidechain and backbone flexibility

von Hallen, Mark A., Keedy, Daniel A., Donald, Bruce R.
Veröffentlicht 2012

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

von Keedy, Daniel A., Fraser, James S., van den Bedem, Henry
Veröffentlicht in PLoS Comput Biol (2015)

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

von Headd, Jeffrey J., Immormino, Robert M., Keedy, Daniel A., Emsley, Paul, Richardson, David C., Richardson, Jane S.
Veröffentlicht 2008

The Role of Local Backrub Motions in Evolved and Designed Mutations

von Keedy, Daniel A., Georgiev, Ivelin, Triplett, Edward B., Donald, Bruce R., Richardson, David C., Richardson, Jane S.
Veröffentlicht 2012

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

von Russi, Silvia, González, Ana, Kenner, Lillian R., Keedy, Daniel A., Fraser, James S., van den Bedem, Henry
Veröffentlicht in J Synchrotron Radiat (2017)

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

von Ebrahim, Ali, Riley, Blake T., Kumaran, Desigan, Andi, Babak, Fuchs, Martin R., McSweeney, Sean, Keedy, Daniel A.
Veröffentlicht in bioRxiv (2021)

Alternate states of proteins revealed by detailed energy landscape mapping

von Tyka, Michael D., Keedy, Daniel A., André, Ingemar, DiMaio, Frank, Song, Yifan, Richardson, David C., Richardsonb, Jane S., Baker, David
Veröffentlicht 2010

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

von Keedy, Daniel A., van den Bedem, Henry, Sivak, David A., Petsko, Gregory A., Ringe, Dagmar, Wilson, Mark A., Fraser, James S.
Veröffentlicht 2014

MolProbity: all-atom structure validation for macromolecular crystallography

von Chen, Vincent B., Arendall, W. Bryan, Headd, Jeffrey J., Keedy, Daniel A., Immormino, Robert M., Kapral, Gary J., Murray, Laura W., Richardson, Jane S., Richardson, David C.
Veröffentlicht 2010

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

von Keedy, Daniel A, Hill, Zachary B, Biel, Justin T, Kang, Emily, Rettenmaier, T Justin, Brandão-Neto, José, Pearce, Nicholas M, von Delft, Frank, Wells, James A, Fraser, James S
Veröffentlicht in eLife (2018)

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

von Riley, Blake T., Wankowicz, Stephanie A., de Oliveira, Saulo H. P., van Zundert, Gydo C. P., Hogan, Daniel W., Fraser, James S., Keedy, Daniel A., van den Bedem, Henry
Veröffentlicht in Protein Sci (2020)

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

von Gainza, Pablo, Roberts, Kyle E., Georgiev, Ivelin, Lilien, Ryan H., Keedy, Daniel A., Chen, Cheng-Yu, Reza, Faisal, Anderson, Amy C., Richardson, David C., Richardson, Jane S., Donald, Bruce R.
Veröffentlicht 2013

CryptoSite: Expanding the druggable proteome by characterization and prediction of cryptic binding sites

von Cimermancic, Peter, Weinkam, Patrick, Rettenmaier, T. Justin, Bichmann, Leon, Keedy, Daniel A., Woldeyes, Rahel A., Schneidman-Duhovny, Dina, Demerdash, Omar N., Mitchell, Julie C., Wells, James A., Fraser, James S., Sali, Andrej
Veröffentlicht in J Mol Biol (2016)

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

von Keedy, Daniel A., Williams, Christopher J., Headd, Jeffrey J., Arendall, W. Bryan, Chen, Vincent B., Kapral, Gary J., Gillespie, Robert A., Block, Jeremy N., Zemla, Adam, Richardson, David C., Richardson, Jane S.
Veröffentlicht 2009

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

von van Zundert, Gydo C.P., Hudson, Brandi M., de Oliveira, Saulo H.P., Keedy, Daniel A., Fonseca, Rasmus, Heliou, Amelie, Suresh, Pooja, Borrelli, Kenneth, Day, Tyler, Fraser, James S., van den Bedem, Henry
Veröffentlicht in J Med Chem (2018)

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

von Williams, Christopher J., Headd, Jeffrey J., Moriarty, Nigel W., Prisant, Michael G., Videau, Lizbeth L., Deis, Lindsay N., Verma, Vishal, Keedy, Daniel A., Hintze, Bradley J., Chen, Vincent B., Jain, Swati, Lewis, Steven M., Arendall, W. Bryan, Snoeyink, Jack, Adams, Paul D., Lovell, Simon C., Richardson, Jane S., Richardson, David C.
Veröffentlicht in Protein Sci (2017)

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

von Keedy, Daniel A, Kenner, Lillian R, Warkentin, Matthew, Woldeyes, Rahel A, Hopkins, Jesse B, Thompson, Michael C, Brewster, Aaron S, Van Benschoten, Andrew H, Baxter, Elizabeth L, Uervirojnangkoorn, Monarin, McPhillips, Scott E, Song, Jinhu, Alonso-Mori, Roberto, Holton, James M, Weis, William I, Brunger, Axel T, Soltis, S Michael, Lemke, Henrik, Gonzalez, Ana, Sauter, Nicholas K, Cohen, Aina E, van den Bedem, Henry, Thorne, Robert E, Fraser, James S
Veröffentlicht in eLife (2015)