Kinemage Web Site: Recent / Select Publications

Randy J. Read, Paul D. Adams, W. Bryan Arendall III, Axel T. Brunger, Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, Thomas Lütteke, Zbyszek Otwinowski, Anastassis Perrakis, Jane S. Richardson, William H. Sheffler, Janet L. Smith, Ian J. Tickle, Gert Vriend, and Peter H. Zwart (2011) "A New Generation of Crystallographic Validation Tools for the Protein Data Bank" Structure 19:1395-1412. doi: 10.1016/j.str.2011.08.006 (open access)

Paul D. Adams, Pavel V. Afonine, Gábor Bunkóczi, Vincent B. Chen, Nathaniel Echols, Jeffrey J. Headd, Li-Wei Hung, Swati Jain, Gary J. Kapral, Ralf W. Grosse Kunstleve, Airlie J. McCoy, Nigel W. Moriarty, Robert D. Oeffner, Randy J. Read, David C. Richardson, Jane S. Richardson, Thomas C. Terwilliger, Peter H. Zwart (2011) "The Phenix software for automated determination of macromolecular structures" Methods 55:94-106. doi: 10.1016/j.ymeth.2011.07.005

Jack A. Dunkle, Leyi Wang, Michael B. Feldman, Arto Pulk, Vincent B. Chen, Gary J. Kapral, Jonas Noeske, Jane S. Richardson, Scott C. Blanchard, and Jamie H. Doudna Cate(2011) "Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding" Science 332:981-984. doi: 10.1126/science.1202692

Robert Hoehndorf, Colin Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris J. Mungall, Jane S. Richardson, Jesse Stombaugh, Eric Westhof, Craig L. Zirbel and Neocles B. Leontis (2011) "The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data" Applied Ontology 6:53-89. doi: /10.3233/AO-2011-0082 (open access)

Michael D. Tyka, Daniel A. Keedy, Ingemar André, Frank DiMaio, Yifan Song, David C. Richardson, Jane S. Richardson and David Baker (2011) "Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping" J Mol Biol 405(2):607-618. doi: /10.1016/j.jmb.2010.11.008 (open access)

Paul D. Adams, Pavel V. Afonine, Gábor Bunkóczi, Vincent B. Chen, Ian W. Davis, Nathaniel Echols, Jeffrey J. Headd, Li-Wei Hung, Gary J. Kapral, Ralf W. Grosse-Kunstleve, Airlie J. McCoy, Nigel W. Moriarty, Robert Oeffner, Randy J. Read, David C. Richardson, Jane S. Richardson, Thomas C. Terwilliger and Peter H. Zwart (2010) "PHENIX: a comprehensive Python-based system for macromolecular structure solution" Acta Crystallographica D: Biological Crystallography D66:213-221. doi: 10.1107/S0907444909052925 (open access)

Jeffrey J. Headd (2009) "Analysis and Error Correction in Structures of Macromolecular Interiors and Interfaces"  Doctoral Dissertation; Computational Biology & Bioinformatics Program; Duke University, 215 pages.

Vincent B. Chen, W. Bryan Arendall III, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson and David C. Richardson (2010) "MolProbity: all-atom structure validation for macromolecular crystallography" Acta Crystallographica D: Biological Crystallography D66:12-21 doi: 10.1107/S0907444909042073 (open access)

Paul D. Adams, Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Randy J. Read, Jane S. Richardson, David C .Richardson and Thomas C. Terwilliger (2009) "Recent developments in phasing and structure refinement for macromolecular crystallography" Current Opinion in Structural Biology 19:566-572 doi: 10.1016/j.sbi.2009.07.014

Vincent B. Chen, Ian Davis and David C. Richardson (2009) "KiNG (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program" Protein Science 18:2403-2409 doi: 10.1002/pro.250 (open access)

Daniel A. Keedy, Christopher J. Williams, Jeffrey J. Headd, W. Bryan Arendall III, Vincent B. Chen, Gary J. Kapral, Robert A. Gillespie, Jeremy N. Block, Adam Zemla, David C. Richardson and Jane S. Richardson (2009) "The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models" Proteins: Structure, Function and Bioinformatics 77(Suppl 9):29-49 doi: 10.1002/prot.22551

Michael L. Tress, Iakes Ezkurdia and Jane S. Richardson (2009) "Target domain definition and classification in CASP8" Proteins: Structure, Function and Bioinformatics 77(Suppl 9):10-17doi: 10.1002/prot.22497

Jane S. Richardson and David C. Richardson (2009)" The Impact of Local Accuracy In Protein and RNA Structures: Validation As an Active Tool" Chapter 15 in Structural Bioinformatics, 2nd Edition, ed. J. Gu and P. Bourne. Wiley (New York).

Jeremy N. Block, David J. Zielinski, Vincent B. Chen, Ian W. Davis, E. Claire Vinson, Rachael Brady, Jane S. Richardson and David C. Richardson (2009) "KinImmerse: Macromolecular VR for NMR ensembles"  Source Code for Biology and Medicine 4:3. doi: 10.1186/1751-0473-4-3 (open access)

Jeffrey J. Headd, Robert M. Immormino, Daniel A. Keedy, Paul Emsley, David C. Richardson and Jane S. Richardson (2009) "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. doi: 10.1007/s10969-008-9045-8 (open access)

Ivelin Georgiev, Daniel Keedy, Jane S. Richardson, David C. Richardson and Bruce R. Donald (2008) "Algorithm for backrub motions in protein design" Bioinformatics 24:i196-i204. doi: 10.1093/bioinformatics/btn169 (open access)

Jane S. Richardson, Bohdan Schneider, Laura W. Murray, Gary J. Kapral, Robert M. Immormino, Jeffrey J. Headd, David C. Richardson, Daniela Ham, Eli Hershkovits, Loren Dean Williams, Kevin S. Keating, Anna Marie Pyle, David Micallef, John Westbrook and Helen M. Berman (2008)  "RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature (an RNA Ontology Consortium contribution)" RNA 14 :465-481. doi: 10.1261/rna.657708 (open access)

X. Wang, G. Kapral, L. Murray, D. Richardson, J. Richardson & J. Snoeyink (2008) "RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone" Journal Mathematical Biology 56:253-278. doi: 10.1007/s00285-007-0082

Ian W. Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura W. Murray, W. Bryan Arendall III, Jack Snoeyink, Jane S. Richardson and David C. Richardson (2007) "MolProbity: all-atom contacts and structure validation for proteins and nucleic acids" Nucleic Acids Research 35 Web Server issue, W375-W383. doi:10.1093/nar/gkm216 (open access)

Laura Weston Murray (2007) "RNA Backbone Rotamers and Chiropraxis" Doctoral Dissertation; Dept. of Biochemistry; Duke University, 169 pages.

Ian W. Davis (2006) "Local Motion and Local Accuracy In Protein Backbone" Doctoral Dissertation; Dept. of Biochemistry; Duke University, 333 pages.

I.W. Davis, W.B. Arendall III, D.C. Richardson, and J.S. Richardson (2006) "The backrub motion: How protein backbone shrugs when a sidechain dances" Structure 14, 265-274. doi:10.1016/j.str.2005.10.007 (Supplementary data available also.)

Neocles B. Leontis, Russ Altman, Helen M. Berman, Steven E. Brenner, James Brown, David Engelke, Stephen C. Harvey, Stephen R. Holbrook, Fabrice Jossinet, Suzanna E. Lewis, François Major, David H. Mathews, Jane S. Richardson, James R. Williamson and Eric Westhof (2006) "The RNA Ontology Consortium: An Open Invitation to the RNA Community" RNA 12, 533-541. doi:10.1261/rna.2343206 (open access)

L.W. Murray, J.S. Richardson, W.B. Arendall III, and D.C. Richardson (2005) "RNA Backbone Rotamers - Finding your way in 7 dimensions. " Biochemical Society Transactions (UK)33, 485-487. PMID: 15916548

W.B. Arendall III, W. Tempel, J.S. Richardson, W. Zhou, S. Wang, I.W. Davis, Z.-J. Liu, J.P. Rose, W.M. Carson, M. Luo, D.C. Richardson, and B-C. Wang (2005) "A test of enhancing model accuracy in high-throughput crystallography." Journal of Structural and Functional Genomics 6, 1-11. doi:10.1007/s10969-005-3138-4

G. Butterfoss, J.S. Richardson, and J. Hermans (2005) "Protein imperfections: separating intrinsic from extrinsic variation of torsion angles." Acta Crystallographica D: Biological Crystallography D61, 88-98. doi:10.1107/S0907444904027325

I.W. Davis, L.W. Murray, J.S. Richardson, and D.C. Richardson (2004) "MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes. " . Nucleic Acids Research 32(Web Server Issue), W615-619. doi:10.1093/nar/gkh398 (open access)

L.L. Videau, W.B. Arendall III, and J.S. Richardson (2004) "The Cis Pro Touch-Turn: A Rare Motif Preferred at Functional Sites" Proteins: Structure, Function and Bioinformatics 56, 298-309. doi:10.1002/prot.20101

W. Tempel, Z.-J.J. Liu, F.D. Schubot, A. Shah, M.V. Weinberg, F.E. Jenney Jr., W.B. Arendall III, M.W.W. Adams, J.S. Richardson, D.C. Richardson, J.P. Rose and B.C. Wang (2004) "Structural Genomics of Pyrococcus furiosus: X-Ray Crystallography Reveals 3D Domain Swapping in Rubrerythrin." Proteins: Structure, Function and Bioinformatics 57, 878-882. doi:10.1002/prot.20280

T.E. Wales, J.S. Richardson, and M.C. Fitzgerald (2004) "Facile Chemical Synthesis and Equilibrium Properties of CopG" Protein Science 13, 1918-1926. doi: 10.1110/ps.04671804

G.T. Kapp, J.S. Richardson, and T.G. Oas (2004) "Kinetic Role of Helix Caps in Protein Folding is Context-Dependent" Biochemistry 43, 3814-3823. doi:10.1021/bi035683k

L.J. Murray, W.B. Arendall III, D.C. Richardson, and J.S. Richardson (2003) "RNA Backbone Is Rotameric" PNAS-USA 100, 13904-13909. doi:10.1073/pnas.1835769100

S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson (2003) "Structure Validation by Cα Geometry: φ,ψ and Cβ Deviation." Proteins: Structure, Function and Genetics 50, 437-450. doi:10.1002/prot.10286

J. S. Richardson, W.B. Arendall III, and D. C. Richardson (2003) "New Tools and Data for Improving Structures, Using All-Atom Contacts. " Chapter in Methods in Enzymology: Macromolecular Crystallography, Part D, ed. C.W. Carter, Jr and R.M. Sweet. Academic Press (San Diego)374, 385-412.

J.S. Richardson and D. C. Richardson (2003) "High-Grade Ore for Data Mining in 3D Structures." in Computational Biology and Genome Informatics, eds. J.T.L. Wang, C.H. Wu, and P.P. Wang. World Scientific Publishing Company (London) pp 139-161.

J. S. Richardson and D. C. Richardson (2002) "Natural β-Sheet Proteins Use Negative Design to Avoid Edge-to-Edge Aggregation." PNAS-USA 99, 2754-2759. doi:10.1073/pnas.052706099

D. C. Richardson and J. S. Richardson (2002) "Teaching Molecular 3-D Literacy." Biochemistry and Molecular Biology Education 30, 21-26. doi:10.1002/bmb.2002.494030010005

D. C. Richardson and J. S. Richardson (2001) "MAGE, PROBE, and Kinemages." In International Tables for Crystallography, ed. M.G. Rossmann and E. Arnold vol. F, chapter 25.2.8.,, 727-730 Kluwer Publishers (Dordrecht).

J. Michael Word (2000) "All-Atom Small-Probe Contact Surface Analysis: An information-rich description of molecular goodness-of-fit" Doctoral Dissertation; Dept. of Biochemistry; Duke University, 273 pages.

J. M. Word, R. C. Bateman Jr., B. K. Presley, S. C. Lovell, and D. C. Richardson (2000) "Exploring steric constraints on protein mutations using MAGE/PROBE." Protein Sci 9, 2251-2259.

S. C. Lovell, J. M. Word, J. S. Richardson, and D. C. Richardson (2000) "The Penultimate Rotamer Library." Proteins: Struct Function and Genetics 40, 389-408. doi: 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2

J. M. Word, S. C. Lovell, T. H. LaBean, H. C. Taylor, M. E. Zalis, B. K. Presley, J. S. Richardson, and D. C. Richardson (1999) "Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms." JMB 285, 1711-33. doi:10.1006/jmbi.1998.2400

J. M. Word, S. C. Lovell, J. S. Richardson, and D. C. Richardson (1999) "Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide Orientation." JMB 285, 1735-47. doi:10.1006/jmbi.1998.2401

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J.S. Richardson (1981 & 2004-2006) "The Anatomy and Taxonomy of Protein Structure" (and updates) In Advances in Protein Chemistry, ed. C.B. Anfinsen, John T. Edsall, Frederic M. Richards. (updates & original on our website) 34, 167-339 Academic Press.