KinImmerse: Macromolecular VR for NMR ensembles

Source Code for Biology and Medicine

Volumn 4, Issue , 2009, Pages

  Block, Jeremy N ^a   Zielinski, David J ^b   Chen, Vincent B ^a   Davis, Ian W ^a,c   Claire, E Claire ^b   Brady, Rachael ^b   Richardson, Jane S ^a   Richardson, David C ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b USA   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 62149145455     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-4-3     Document Type: Article

References (50)

1. Richardson DC Richardson JS Teaching molecular 3-D literacy Biochem Molec Biol Educ 2002, 30:21-26. 10.1002/bmb.2002.494030010005
2. Katz L Levinthal C Interactive computer graphics and representation of complex biological structures Ann Rev Biophys Bioengin 1972, 1:465-504. 4567757
3. Porter TK Spherical shading Computer Graphics 1978, 12:282-285.
4. Britton EG Lipscomb JL Pique ME Making nested rotations convenient for the user Computer Graphics 1978, 12:222-227.
5. Jones TA A graphics model building and refinement system for macromolecules J Applied Crystallogr 1978, 11:268-272.
6. Connolly ML Solvent-accessible surfaces of proteins and nucleic acids Science 1993, 221(4612):709-713. 6879170
7. Richardson JS The Anatomy and Taxonomy of Protein Structure Adv Prot Chem 1981, 34:167-339. http://kinemage.biochem.duke.edu/teaching/anatax/ 7020376
8. Carson WM Bugg CE Algorithm for ribbon models of proteins J Molec Graphics 1986, 4:121-122.
9. Richardson DC Richardson JS The kinemage: A tool for scientific illustration Protein Science 1992, 1:3-9. 2142077 1304880
10. Sayle R Milner-White EJ RASMOL: Biomolecular graphics for all Trends Biochem Sci 1995, 20(9):374. 7482707
11. DeLano WL The PyMOL molecular graphics system DeLano Scientific, Palo Alto, CA, USA 2002.
12. Guex N Peitsch MC SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling Electrophoresis 1997, 18:2714-2723. 9504803
13. Lovell SC Davis IW Arendall WB III de Bakker PIW Word JM Prisant MG Richardson JS Richardson DC Structure validation by Cα geometry: φ, ψ and Cβ deviation Proteins 2003, 50(3):437-450. 12557186
14. Pettersen EF Goddard TD Huang CC Couch GS Greenblatt DM Meng EC Ferrin TE UCSF Chimera - A visualization system for exploratory research and analysis J Comput Chem 2004, 25:1605-1612. 15264254
15. Koradi R Billeter M Wüthrich K MOLMOL: A program for display and analysis of macromolecular structures J Mol Graphics 1996, 14(1):51-55. 8744573
16. Emsley P Cowtan K Coot: Model-building tools for molecular graphics Acta Crystallogr 2004, 60(Pt 12 Pt 1):2126-2132. 15572765
17. Humphrey W Dalke A Schulten K VMD - visual molecular dynamics J Molec Graphics 1996, 14:33-38.
18. Sherman WR Craig AB Understanding Virtual Reality: Interface, Application, and Design San Francisco: Morgan Kauffmann 2002.
19. Arthur K Preston T Taylor RM II Brooks FP Jr Whitton MC Wright WV The PIT: Design, Implementation, and Next Steps Proceedings of the 2nd International Immersive Projection Technology Workshop Ames, Iowa 1998.
20. Surles MC Richardson JS Richardson DC Brooks FP Jr Sculpting proteins interactively: Continual energy minimization embedded in a graphical modeling system Protein Sci 1994, 3:198-210. 2142792 8003957
21. Taylor RM II Robinett W Chi VL Brooks FP Jr Wright WV Williams RS Snyder EJ The Nanomanipulator: A Virtual-Reality Interface for a Scanning Tunneling Microscope ACM SIGGRAPH Proc 1993, 93:127-34.
22. Fisher J Cummings J Desai KV Vicci L Wilde B Keller K Weigle C Bishop G Taylor RM II Davis CW Boucher R O'Brien ET Superfine R Three-dimensional force microscope: A nanometric optical tracking and magnetic manipulation system for the biomedical sciences Rev Scientific Instruments 2005, 76:53711-22.
23. Brady R Pixton J Baxter G Moran P Potter CS Carragher B Belmont A Crumbs: A virtual tracking tool for biological imaging Proceedings of the 1995 Biomedical Visualization Conference Washington DC: IEEE Computer Society 1995:18.
24. Cruz-Neira C Sandin D DeFanti T Surround-screen projection-based virtual reality: The design and implementation of the CAVE ACM SIGGRAPH Proc 1993, 93:135-142.
25. Sherman W FreeVR Home Page http://www.freevr.org
26. Stone J VMD Publications http://www.ks.uiuc.edu/Research/vmd/ publications/cave2001.pdf http://www.ks.uiuc.edu/Research/vmd/ publications/uct2008vmdviz.pdf
27. Ferey N Delalande O Grasseau G Baaden M A VR framework for interacting with molecular simulations Proceedings of the ACM Symposium on Virtual Reality Software & Technology Bordeaux, France. VRST 2008:91-94.
28. Moritz E Meyer J Interactive protein structure visualization using virtual reality Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering 2004:503-507.
29. PDB and CalIT2 PDB in a CAVE: Virtual reality environment highlights PDB structures PDB Newsletter spring 2006, 29:1.
30. Jean Goldwurm 3D Visualization Theater http://www.weizmann.ac.il/ISPC/ 3dtheater/index.html
31. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The Protein Data Bank Nucleic Acids Res 2000, 28:235-242. 102472 10592235
32. Cavanagh J Fairbrother WJ Palmer AG III Rance M Skelton NJ Protein NMR Spectroscopy: Principles and Practice San Diego: Academic Press 2 2006.
33. Word JM Lovell SC LaBean TH Zalis ME Presley BK Richardson JS Richardson DC Visualizing and Quantitating Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms J Mol Biol 1999, 285:1711-1733. 9917407
34. Davis IW Leaver-Fay A Chen VB Block JN Kapral GJ Wang X Murray LW Arendall WB III Snoeyink J Richardson JS Richardson DC MolProbity: All-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res 2007, 35:W375-W383. 1933162 17452350
35. Arendall WB III Tempel W Richardson JS Zhou W Wang S Davis IW Liu Z-J Rose JP Carson WM Luo M Richardson DC Wang B-C A test of enhancing model accuracy in high-throughput crystallography J Struct Funct Genomics 2005, 6:1-11. 15965733
36. 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 J Struct Funct Genomics 2008. published on-line 11 November 2008 (open access) 19002604
37. Richardson DC Richardson JS MAGE, PROBE, and Kinemages Chapter 25.2.8 in IUCr's International Tables for Crystallography, Volume F: Crystallography of Biological Macromolecules Dortrecht: Kluwer Academic Press Rossmann M, Arnold E 2001.
38. Schaeffer B Goudeseune C Syzygy: Native PC cluster VR Technical report from the Integrated Systems Laboratory Beckman Institute, U IL Urbana-Champaign 2003. http://www.isl.uiuc.edu/szg/
39. Taylor RM II Hudson TC Seeger A Weber H Juliano J Helser AT VRPN: A device-independent, network-transparent VR peripheral system Proceedings of the ACM Symposium on Virtual Reality Software & Technology: 2008 Banff Centre, Canada. VRST 2001.
40. Mechdyne http://www.mechdyne.com/integratedSolutions/software/products/ trackd/trackd.htm
41. Kilgard MJ The OpenGL utility toolkit (GLUT) programming interface: API version 3 Silicon Graphics Incorporated 1996.
42. Cornilescu G Marquardt JL Ottiger M Bax A Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase J Amer Chem Soc 1998, 120:6836-6837.
43. Zheng D Aramini JM Montelione GT Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data Protein Sci 2004, 13:549-554. 2286702 14718654
44. Bomar MG Pai MT Tzeng SR Li SS Zhou P Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase eta Embo Reports 2007, 8:247-251. 1808033 17304240
45. Losonczi JA Andrec M Fischer MWF Prestegard JH Order matrix analysis of residual dipolar couplings using singular value decomposition J Magn Reson 1999, 138(2):334-342. 10341140
46. Yan AK Langmead CJ Donald BR A probability-based similarity measure for Saupe alignment tensors with applications to residual dipolar couplings in NMR structural biology Internat J Robotics Res 2005, 24:165-182.
47. Wedemeyer WJ Rohl CA Scheraga HA Exact solutions for chemical bond orientations from residual dipolar couplings J Biomolec NMR 2002, 22(2):137-151. 11883775
48. Saupe A Recent results in the field of liquid crystals Angewandte Chemie 1968, 7:97112.
49. Ban YA Edelsbrunner H Rudolph J Interface surfaces for protein-protein complexes Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology 2004:205-212.
50. Huang YJ Powers R Montelione GT Protein NMR recall, precision, and F-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics J Am Chem Soc 2005, 127(6):1665-1674. 15701001