Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study

le Fusco, Diana, Headd, Jeffrey J., De Simone, Alfonso, Wang, Jun, Charbonneau, Patrick
Foilsithe 2014

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

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

Improved low-resolution crystallographic refinement with Phenix and Rosetta

le DiMaio, Frank, Echols, Nathaniel, Headd, Jeffrey J, Terwilliger, Thomas C, Adams, Paul D, Baker, David
Foilsithe 2013

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement

le Headd, Jeffrey J., Echols, Nathaniel, Afonine, Pavel V., Moriarty, Nigel W., Gildea, Richard J., Adams, Paul D.
Foilsithe 2014

Interactive comparison and remediation of collections of macromolecular structures

le Moriarty, Nigel W., Liebschner, Dorothee, Klei, Herbert E., Echols, Nathaniel, Afonine, Pavel V., Headd, Jeffrey J., Poon, Billy K., Adams, Paul D.
Foilsithe in Protein Sci (2017)

MolProbity: all-atom structure validation for macromolecular crystallography

le 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.
Foilsithe 2010

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

le Headd, Jeffrey J., Echols, Nathaniel, Afonine, Pavel V., Grosse-Kunstleve, Ralf W., Chen, Vincent B., Moriarty, Nigel W., Richardson, David C., Richardson, Jane S., Adams, Paul D.
Foilsithe 2012

Towards automated crystallographic structure refinement with phenix.refine

le Afonine, Pavel V., Grosse-Kunstleve, Ralf W., Echols, Nathaniel, Headd, Jeffrey J., Moriarty, Nigel W., Mustyakimov, Marat, Terwilliger, Thomas C., Urzhumtsev, Alexandre, Zwart, Peter H., Adams, Paul D.
Foilsithe 2012

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

le Afonine, Pavel V., Grosse-Kunstleve, Ralf W., Chen, Vincent B., Headd, Jeffrey J., Moriarty, Nigel W., Richardson, Jane S., Richardson, David C., Urzhumtsev, Alexandre, Zwart, Peter H., Adams, Paul D.
Foilsithe 2010

Co-Crystal Structures of PKG Iβ (92–227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding

le Kim, Jeong Joo, Casteel, Darren E., Huang, Gilbert, Kwon, Taek Hun, Ren, Ronnie Kuo, Zwart, Peter, Headd, Jeffrey J., Brown, Nicholas Gene, Chow, Dar-Chone, Palzkill, Timothy, Kim, Choel
Foilsithe 2011

The crystal structures of PKG Iβ (92-227) with cGMP and cAMP reveal the molecular details of cyclic-nucleotide binding

le Kim, Jeong Joo, Casteel, Darren E, Huang, Gilbert, Kwon, Taek Hun, Ren, Ronnie Kuo, Zwart, Peter, Headd, Jeffrey J, Brown, Nicholas Gene, Chow, Dar-Chone, Palzkill, Timothy, Kim, Choel
Foilsithe 2011

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

le 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.
Foilsithe 2009

IMP1 3′ UTR shortening enhances metastatic burden in colorectal cancer

le Andres, Sarah F, Williams, Kathy N, Plesset, Jacqueline B, Headd, Jeffrey J, Mizuno, Rei, Chatterji, Priya, Lento, Ashley A, Klein-Szanto, Andres J, Mick, Rosemarie, Hamilton, Kathryn E, Rustgi, Anil K
Foilsithe in Carcinogenesis (2019)

Automating crystallographic structure solution and refinement of protein–ligand complexes

le Echols, Nathaniel, Moriarty, Nigel W., Klei, Herbert E., Afonine, Pavel V., Bunkóczi, Gábor, Headd, Jeffrey J., McCoy, Airlie J., Oeffner, Robert D., Read, Randy J., Terwilliger, Thomas C., Adams, Paul D.
Foilsithe 2013

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

le Richardson, Jane S., Schneider, Bohdan, Murray, Laura W., Kapral, Gary J., Immormino, Robert M., Headd, Jeffrey J., Richardson, David C., Ham, Daniela, Hershkovits, Eli, Williams, Loren Dean, Keating, Kevin S., Pyle, Anna Marie, Micallef, David, Westbrook, John, Berman, Helen M.
Foilsithe 2008

Graphical tools for macromolecular crystallography in PHENIX

le Echols, Nathaniel, Grosse-Kunstleve, Ralf W., Afonine, Pavel V., Bunkóczi, Gábor, Chen, Vincent B., Headd, Jeffrey J., McCoy, Airlie J., Moriarty, Nigel W., Read, Randy J., Richardson, David C., Richardson, Jane S., Terwilliger, Thomas C., Adams, Paul D.
Foilsithe 2012

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

le 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.
Foilsithe in Protein Sci (2017)

PHENIX: a comprehensive Python-based system for macromolecular structure solution

le Adams, Paul D., Afonine, Pavel V., Bunkóczi, Gábor, Chen, Vincent B., Davis, Ian W., Echols, Nathaniel, Headd, Jeffrey J., Hung, Li-Wei, Kapral, Gary J., Grosse-Kunstleve, Ralf W., McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert, Read, Randy J., Richardson, David C., Richardson, Jane S., Terwilliger, Thomas C., Zwart, Peter H.
Foilsithe 2010

The Phenix Software for Automated Determination of Macromolecular Structures

le Adams, Paul D., Afonine, Pavel V., Bunkóczi, Gábor, Chen, Vincent B., Echols, Nathaniel, Headd, Jeffrey J., Hung, Li-Wei, Jain, Swati, Kapral, Gary J., Grosse Kunstleve, Ralf W., McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert D., Read, Randy J., Richardson, David C., Richardson, Jane S., Terwilliger, Thomas C., Zwart, Peter H.
Foilsithe 2011