Applying forces to elastic network models of large biomolecules using a haptic feedback device

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 3, 2011, Pages 203-211

  Stocks, M B ^a   Laycock, S D ^a   Hayward, S ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

Force feedback; Normal mode analysis; Protein flexibility

Indexed keywords

CONFORMATIONS; EIGENVALUES AND EIGENFUNCTIONS; HAPTIC INTERFACES; MAMMALS; MOLECULES;

APPLIED FORCES; CONFORMATIONAL CHANGE; ELASTIC NETWORK MODELS; FORCE-FEEDBACK; HAPTIC FEEDBACK DEVICES; INTUITIVE EXPLORATION; LARGE BIOMOLECULES; NORMAL MODE ANALYSIS; NORMAL MODES; PROTEIN FLEXIBILITY;

BIOMOLECULES;

ALCOHOL DEHYDROGENASE; ASPARTATE CARBAMOYLTRANSFERASE; CHAPERONIN; FERRITIN; GLUTAMATE AMMONIA LIGASE; HYDROLASE; S ADENOSYLHOMOCYSTEINE; SEED STORAGE PROTEIN;

ARTICLE; COMPUTER INPUT DEVICE; COMPUTER INTERFACE; COMPUTER MEMORY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; ELASTIC NETWORK MODEL; INTERMETHOD COMPARISON; MACROMOLECULE; MATERIALS TESTING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; TACTILE FEEDBACK;

EID: 79956008644     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-010-9410-0     Document Type: Article

References (37)

1. Tirion M (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905-1908
2. Chacon P, Tama F, Wriggers W (2003) Mega-dalton biomolecular motion captured from electron microscopy reconstructions. J Mol Biol 326:485-492 (Pubitemid 36279342)
3. Wang Y, Rader AJ, Bahar I, Jernigan RL (2004) Global ribosome motions revealed with elastic network model. J Struct Biol 147:302-314 (Pubitemid 39140737)
4. Bahar I, Rader AJ (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 15:586-592 (Pubitemid 41393491)
5. Lezon TR, Sali A, Bahar I (2009) Global motions of the nuclear pore complex: insights from elastic network models. PLoS Comput Biol 5
6. Atsushi M, Ishida H (2009) Global conformational changes of ribosome observed by normal mode fitting for 3D cryo-EM structures. Structure 17:1605-1613
7. Bahar I, Lezon TR, Bakan A, Shrivastava IH (2009) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 110:1605-1613
8. Tama F, Sanejouand Y-H (2001) Conformational change of proteins arising from normal mode calculations. Prot Eng 14:1-6 (Pubitemid 32318932)
9. Hayward S (2004) Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. J Mol Biol 339:1001-1021
10. Ikeguchi M, Ueno J, Sato M, Kidera A (2005) Protein structural change upon ligand binding: linear response theory. Phys Rev Lett 94:078102-1-4 (Pubitemid 40620748)
11. Hayward S, Kitao A (2006) Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase. Biophys J 91:1823-1831 (Pubitemid 44352446)
12. Atilgan C, Atilgan AR (2009) Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PLoS Comput Biol 5
13. Eyal E, Bahar I (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models. Biophys J 94:3424-3435
14. Brooks FP, Ouh-Young M, Battert JJ, Kilpatrick PJ (1990) Project GROPE-haptic displays for scientific visualization. Comput Graph 24:177-185
15. Comai S, Mazza D (2010) A haptic-based framework for chemistry education: experiencing molecular interactions with touch, technology enhanced learning. Quality of teaching and educational reform. Springer, Berlin Heidelberg, pp 338-344
16. Nagata H, Mizushima H, Tanaka H (2002) Concept and prototype of protein-ligand docking simulator with force feedback technology. Bioinformatics 18:140-146 (Pubitemid 34145042)
17. Sankaranarayanan G, Weghorst S, Sanner M, Gillet A, Olson A (2003) Role of haptics in teaching structural molecular biology. HAPTICS '03, 363
18. Wollacott AM, Merz KM Jr. (2006) Haptic applications for molecular structure manipulation. J Mol Graph Model 25:801-805
19. Subasi E, Basdogan C (2008) A new haptic interaction and visualization approach for rigid molecular docking in virtual environments. Presence Teleoper Virtual Environ 17:73-90
20. Stocks M, Hayward S, Laycock S (2009) Interacting with the biomolecular solvent accessible surface via a haptic feedback device. BMC Struct Biol 9:69
21. Daunay B, Régnier S (2009) Stable six degrees of freedom haptic feedback for flexible ligand-protein docking. Computer-Aided Design, pp 886-895
22. Stone J, Gullingsrud J, Grayson P, Schulten K (2001) A system for interactive molecular dynamics simulation. ACM Siggraph, pp 191-194
23. Bolopion A, Cagneau B, Redon S, Régnier S (2010) Comparing position and force control for interactive molecular simulators with haptic feedback. J Mol Graph Model 29(2):280-289
24. Rossi R, Isorce M, Morin S, Flocard J, Arumugan K, Crouzy S, Vivaudou M, Redon S (2007) Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design. Bioinformatics 23(13):408-417
25. Nishikawa T, Go N (1987) Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property. Proteins Struct Funct Genet 2:308-329
26. Go N (1990) A theorem on amplitudes of thermal atomic fluctuations in large molecules assuming specific conformations calculated by normal mode analysis. Biophys Chem 35:105-112
27. Hayward S, Go N (1995) Collective variable description of native protein dynamics. Ann Rev Phys Chem 46:223-250
28. Kitao A, Hirata F, Go N (1991) The effects of solvent on the conformation and the collective motions of protein - normal mode analysis and molecular-dynamics simulations of melittin in water and in vacuum. Chem Phys 158:447-472
29. García AE (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68:2696-2699
30. Amadei A, Linssen ABM, Berendsen HJC (1993) Essential dynamics of proteins. Proteins Struct Funct Genet 17:412-425 (Pubitemid 23358549)
31. Hayward S, Kitao A, Hirata F, Go N (1993) Effect of solvent on collective motions in globular proteins. J Mol Biol 234:1207-1217 (Pubitemid 24027248)
32. Kitao A, Go N (1999) Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol 9:164-169 (Pubitemid 29452893)
33. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80:505-515
34. Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding Design 2:173-181 (Pubitemid 127740467)
35. Karsten S, Yves-Henri S (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucl Acids Res 32:W610-614
36. Laycock SD, Stocks MB, Hayward S (2010) Navigation and exploration of large data-sets using a haptic feedback device. SIGGRAPH '10: ACM SIGGRAPH 2010 Posters
37. Zilles CB, Salisbury JK (1995) A constraint based God-object method for haptic display. In: Proceedings of the IEEE conference on intelligent robots and systems, pp 146-151