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

Por Hallen, Mark A., Keedy, Daniel A., Donald, Bruce R.
Publicado em 2012

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

Por Keedy, Daniel A., Fraser, James S., van den Bedem, Henry
Publicado no PLoS Comput Biol (2015)

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

Por Headd, Jeffrey J., Immormino, Robert M., Keedy, Daniel A., Emsley, Paul, Richardson, David C., Richardson, Jane S.
Publicado em 2008

The Role of Local Backrub Motions in Evolved and Designed Mutations

Por Keedy, Daniel A., Georgiev, Ivelin, Triplett, Edward B., Donald, Bruce R., Richardson, David C., Richardson, Jane S.
Publicado em 2012

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

Por Russi, Silvia, González, Ana, Kenner, Lillian R., Keedy, Daniel A., Fraser, James S., van den Bedem, Henry
Publicado no J Synchrotron Radiat (2017)

Alternate states of proteins revealed by detailed energy landscape mapping

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

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

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

MolProbity: all-atom structure validation for macromolecular crystallography

Por 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.
Publicado em 2010

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

Por 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.
Publicado em 2013

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

Por 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
Publicado no J Mol Biol (2016)

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

Por 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.
Publicado em 2009

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

Por 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
Publicado no eLife (2015)