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Jeffrey J. Headd, Ph.D. - Publications

Affiliations: 
2009 Computational Biology and Bioinformatics Duke University, Durham, NC 
Area:
3D structures of proteins
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20 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
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  0.693
2017 Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd J, Poon BK, Adams PD. Interactive Comparison and Remediation of Collections of Macromolecular Structures. Protein Science : a Publication of the Protein Society. PMID 28901593 DOI: 10.1002/Pro.3296  0.752
2014 Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. Acta Crystallographica. Section D, Biological Crystallography. 70: 1346-56. PMID 24816103 DOI: 10.1107/S1399004714003277  0.737
2014 Fusco D, Headd JJ, De Simone A, Wang J, Charbonneau P. Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study. Soft Matter. 10: 290-302. PMID 24489597 DOI: 10.1039/C3Sm52175C  0.357
2014 Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Automating crystallographic structure solution and refinement of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography. 70: 144-54. PMID 24419387 DOI: 10.1107/S139900471302748X  0.74
2013 DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods. 10: 1102-4. PMID 24076763 DOI: 10.1107/S2053273314092171  0.731
2012 Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD. Graphical tools for macromolecular crystallography in PHENIX. Journal of Applied Crystallography. 45: 581-586. PMID 22675231 DOI: 10.1107/S0021889812017293  0.717
2012 Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallographica. Section D, Biological Crystallography. 68: 381-90. PMID 22505258 DOI: 10.1107/S0907444911047834  0.754
2012 Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallographica. Section D, Biological Crystallography. 68: 352-67. PMID 22505256 DOI: 10.1107/S0907444912001308  0.76
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  0.654
2011 Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, et al. The Phenix software for automated determination of macromolecular structures. Methods (San Diego, Calif.). 55: 94-106. PMID 21821126 DOI: 10.1016/J.Ymeth.2011.07.005  0.772
2011 Kim JJ, Casteel DE, Huang G, Kwon TH, Ren RK, Zwart P, Headd JJ, Brown NG, Chow D, Palzkill T, Kim C. The crystal structures of PKG Iβ (92-227) with cGMP and cAMP reveal the molecular details of cyclic-nucleotide binding Bmc Pharmacology. 11: 1-3. DOI: 10.1186/1471-2210-11-S1-O14  0.355
2011 Echols N, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Headd JJ, Hung L-, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, et al. Graphical tools for structure determination and refinement inPHENIX Acta Crystallographica Section a Foundations of Crystallography. 67: C161-C162. DOI: 10.1107/S0108767311096024  0.741
2010 Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. Journal of Applied Crystallography. 43: 669-676. PMID 20648263 DOI: 10.1107/S0021889810015608  0.654
2010 Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica. Section D, Biological Crystallography. 66: 213-21. PMID 20124702 DOI: 10.1107/S0907444909052925  0.747
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  0.667
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  0.569
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  0.593
2008 Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM, et al. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). Rna (New York, N.Y.). 14: 465-81. PMID 18192612 DOI: 10.1261/Rna.657708  0.539
2007 Headd JJ, Ban YE, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. Protein-protein interfaces: properties, preferences, and projections. Journal of Proteome Research. 6: 2576-86. PMID 17542628 DOI: 10.1021/Pr070018+  0.346
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