JavaMage
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JavaMage is the earliest and simplest version of our interactive web graphics. The Java picture is a "kinemage" (kinetic image). To rotate in 3-D, drag slowly with the mouse. To identify a point, click on it; to measure a distance, click on each end point. To see the fuller implementation in KiNG, try the MolProbity link above.
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Research Interests
The long-term goal of the Richardson lab is to contribute to a deeper understanding of the 3D structures of proteins, including their description, determinants, folding, evolution, and control. This has now been broadened to include RNA structures. Our approaches include structural bioinformatics, macromolecular crystallography, molecular graphics, analysis of structures, and methods development, currently focussed on the improvement of structural accuracy.
Following on two of the earliest protein crystallographic structures (Staphylococcal nuclease and Cu,ZN superoxide dismutase), our continuing analysis and comparison of protein structures then led to an early classification system, new overall folds (such as the Greek key beta barrel, and what is now called the SS beta cross), and description of many new small-scale features (such as right-handed crossovers, beta bulges, helix N-caps and C-caps, and cisPro touch-turns). We now also analyze structural motifs in RNA, including an all-angle definition of conformers for RNA backbone.
We develop methods for representing protein structure, most notably the hand drawings that popularized ribbon schematics and formed the basis for the present computer ribbon drawings. We develop software to fill what we see as unmet needs, most notably kinemages (molecular graphics optimized for the communication of specific ideas in 3D) and the associated Mage and KiNG display programs, free software on Mac, PC, and Linux, widely used for teaching and databases as well as for research. Mage and KiNG incorporate many functions for analyzing and rebuilding macromolecules, including the "Backrub" tool for making realistic local movements in protein backbone.
We were among the first groups to do protein de novo design and made designs in all 4 of the major tertiary-structure types, using complex, native-like sequences (e. g., betabellin, Felix, babarellin, and SScorin). We introduced the concept of negative design, and we first pointed out the general problem of the more-or-less molten nature of most fully de novo designs. In order to treat internal packing in quantitative detail, we developed an all-atom contact algorithm to quantify and visualize the geometric details of molecular interaction; it uses all explicit H atoms and a very small probe sphere to show those surface patches where atoms are within 0.5 Å of exact van der Waals contact. This method gives a sensitive description of packing quality within or between molecules, for use in protein or drug design, for understanding structural features and interactions, and for designing non-disruptive mutations. All-atom contact analysis, along with crystallographic B-factors, allowed us to construct much-improved libraries and data distributions for protein sidechain rotamers and Ramachandran phi,psi backbone angles. All of these validation analyses can be run interactively on the MolProbity web service, including optimized hydrogen addition and automated correction of "flipped" sidechain amide or histidine orientations.
All-atom steric clashes are a powerful and sensitive way of finding problems in molecular structures, and even of suggesting how to make corrections. As part of the SECSG structural genomics effort, we used MolProbity diagnosis along with rebuilding and refinement on 29 SECSG structures, producing modest improvements in traditional crystallographic measures (R, Rfree, geometry, real-space residual) and dramatic order-of-magnitude improvements in all-atom clashscore and rotamer and Ramachandran outliers. We are now working to extend applicability to RNA and to NMR structures, and, as part of the PHENIX software team, to further integrate and automate these techniques in crystallography. A long-term vision is to enable the determination of accurate models even from low-resolution data.
Recent Publications (from "about us/papers" in the kinemage web site)
(2.7MB)
2009Bourne |
Book Link |
J.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). |
(1.1MB)
2009Block |
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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) |
(437KB)
2008Headd |
SuppData |
Jeffrey J. Headd, Robert M. Immormino, Daniel A. Keedy, Paul Emsley, David C. Richardson and Jane S. Richardson (2008) "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) |
(488KB)
2008Georgiev |
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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 |
(1.1MB)
2008ROC |
SuppData |
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) |
(868KB)
2008Wang |
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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 |
(2.2MB)
2007Davis |
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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 |
(17.1MB)
2007Murray |
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Laura Weston Murray (2007) "RNA Backbone Rotamers and Chiropraxis" Doctoral Dissertation; Dept. of Biochemistry; Duke University, 169 pages. handle:10161/382 |
(17.6MB)
2006Davis |
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Ian W. Davis (2006) "Local Motion and Local Accuracy In Protein Backbone" Doctoral Dissertation; Dept. of Biochemistry; Duke University, 333 pages. handle:10161/5 |
(464KB)
2006Davis |
SuppData &
hi-res img |
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.) |
(596KB)
2006ROC |
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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) |
(300KB)
2005Murray |
Abstract |
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 |
(368KB)
2005Arendall |
Abstract |
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 |
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Abstract |
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 |
(668KB)
2004Davis |
Abstract |
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) |
(868KB)
2004Videau |
Abstract |
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 |
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Abstract |
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 |
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Abstract |
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 |
(480KB)
2004Kapp |
Abstract |
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 |
(620KB)
2003Murray |
Abstract |
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 |
(790KB)
2003Lovell |
Abstract |
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 |
(780KB)
2003Methods |
Abstract |
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. |
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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. |
(840KB)
2002Richardson |
Abstract |
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 |
(2.2MB)
2002BaMBEd |
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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 |
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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). |
(8.5MB)
2000Word |
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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. |
(188KB)
2000Word |
Abstract |
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. |
(296KB)
2000Lovell |
Abstract |
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 |
(1.4MB)
1999WordA |
Abstract |
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 |
(804KB)
1999WordB |
Abstract |
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. |
For more details, see our kinemage web site at http://kinemage.biochem.duke.edu/, where all our software is available free and open-source, as well as datasets and examples. There is a service called MolProbity where you can run our structure validation tools on an uploaded file of your own or one chosen from the PDB or NDB, and display the results directly on-line in KiNG.
Lab Members (from "about us/contacts" in the kinemage web site)
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| Name |
Position |
Cast of
Characters |
e-mail |
Telephone |
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| David Richardson |
Professor |
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dcr AT kinemage.biochem.duke.edu |
919-684-6010 |
| Jane Richardson |
Professor |
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jsr AT kinemage.biochem.duke.edu |
919-684-6010 |
| Bryan Arendall |
Research Associate |
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arendall AT duke.edu |
919-681-8827 |
| Jeremy Block |
Grad Student (SBB) |
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jeremy.block AT duke.edu |
919-684-6118 |
| Vincent Chen |
Grad Student |
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vincent.chen AT duke.edu |
919-681-8826 |
| Jeff Headd |
Grad Student (CBB/SBB) |
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jeffrey.headd AT duke.edu |
919-684-2217 |
| Gary Kapral |
Grad Student |
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gary.kapral AT duke.edu |
919-681-8826 |
| Daniel Keedy |
Grad Student |
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daniel.keedy AT duke.edu |
919-681-8826 |
| Sandra Morris |
Student |
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sandra.morris AT duke.edu |
919-681-8826 |
| Laura Murray |
Research Associate |
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laura.weston AT duke.edu |
919-681-8826 |
| Lizbeth Videau |
Staff Assistant |
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videau AT biochem.duke.edu |
919-684-6010 |
| Christopher J. Williams |
Grad Student |
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christopher.j.williams AT duke.edu |
919-684-6010 |
Past Lab Members |
| Name |
Currently |
Looked
Like |
e-mail |
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| Ian Davis |
Research Associate
Baker Lab, U.Washington |
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ian.w.davis AT gmail.com |
| Bob Immormino |
Research Associate
Dept Immunology, U.Washington |
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immormino AT gmail.com |
| Thom LaBean |
Associate Research Professor
Computer Science, Duke Univ |
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thl AT cs.duke.edu |
| Simon Lovell |
Faculty of Life Sciences
Univ of Manchester, UK |
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simon.lovell AT man.ac.uk |
| Michael G. Prisant |
Visiting Professor |
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prisant AT cs.duke.edu |
| Xueyi Wang |
Assistant Professor
NW Nazarene U, Nampa,ID |
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xwang AT nnu dot edu |
| J. Michael Word |
Open Eye Software
Santa Fe, NM |
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word27605 AT gmail.com |
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