Kinemage Web Site: Recent / Select Publications

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

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 12 , 533-541.

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. (published online 31 March 07, 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

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. (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.

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.

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.

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.

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.

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.

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.

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

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.

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

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.

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 (2003) "All-Atom Contacts: A New Approach to Structure Validation." Chapter 15 in Structural Bioinformatics (Methods of biochemical analysis; vol 44), ed. P. Bourne and H. Weissig. Wiley (New York).

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.

D. C. Richardson and J. S. Richardson (2002) "Teaching Molecular 3-D Literacy." Biochemistry and Molecular Biology Education 30, 21-26.

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.

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.

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.

. . .
. . .
. . .

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.