AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics

IEEE Transactions on Visualization and Computer Graphics

Volumn 22, Issue 1, 2016, Pages 747-756

  Byška, Jan ^a   Le Muzic, Mathieu ^b   Gröller, M Eduard ^b,c   Viola, Ivan ^b,c   Kozlíková, Barbora ^a,b  

^a MASARYK UNIVERSITY   (Czech Republic)

^b VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

^c UNIVERSITY OF BERGEN   (Norway)

Author keywords

Aerodynamics; Amino acids; Data visualization; Proteins; Shape; Three dimensional displays; Visualization

Indexed keywords

AERODYNAMICS; AMINO ACIDS; DATA VISUALIZATION; FLOW VISUALIZATION; MOLECULAR DYNAMICS; PROTEINS; THREE DIMENSIONAL COMPUTER GRAPHICS; VISUALIZATION;

BASIC PRINCIPLES; CHEMICAL AND PHYSICAL PROPERTIES; CURVATURE INFORMATION; DOMAIN EXPERTS; INTERACTIVE EXPLORATION; PROTEIN FUNCTIONS; SHAPE; TEMPORAL AGGREGATION;

THREE DIMENSIONAL DISPLAYS;

PROTEIN;

AMINO ACID SEQUENCE; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; PROCEDURES; PROTEIN CONFORMATION; SEQUENCE ANALYSIS; SPATIOTEMPORAL ANALYSIS;

AMINO ACID SEQUENCE; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SPATIO-TEMPORAL ANALYSIS;

EID: 84946606231     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2015.2467434     Document Type: Article

References (25)

1. K. Bidmon, S. Grottel, F. Bös, J. Pleiss, and T. Ertl. Visual abstractions of solvent pathlines near protein cavities. Computer Graphics Forum, 27(3):935-942, 2008.
2. J. Byska, A. Jurcik, M. E. Gröller, I. Viola, and B. Kozlikova. MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids. Computer Graphics Forum, 34(3):1-10, 2015.
3. E. Chovancova, A. Pavelka, P. Benes, O. Strnad, J. Brezovsky, B. Kozlikova, A. Gora, V. Sustr, M. Klvana, P. Medek, L. Biedermannova, J. Sochor, and J. Damborsky. CAVER 3.0: A tool for the analysis of transport pathways in dynamic protein structures. PLoS Computational Biology, 8(10), 2012.
4. U. Hensen, T. Meyer, J. Haas, R. Rex, G. Vriend, and H. Grubmueller. Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. PLoS ONE, 7(5):e33931, 2012.
5. H. Hochheiser and B. Shneiderman. Dynamic query tools for time series data sets, timebox widgets for interactive exploration. Information Visualization, 3(1):1-18, 2004.
6. W. Hong, X. Gu, F. Qiu, M. Jin, and A. Kaufman. Conformal virtual colon flattening. In Proceedings of the 2006 ACM Symposium on Solid and Physical Modeling, SPM '06, pages 85-93, New York, NY, USA, 2006. ACM.
7. A. Kanitsar, D. Fleischmann, R. Wegenkittl, P. Felkel, and M. Gröller. CPR - curved planar reformation. In Visualization, 2002. VIS 2002. IEEE, pages 37-44, Nov 2002.
8. M. Klvana, M. Pavlova, T. Koudelakova, R. Chaloupkova, P. Dvorak, Z. Prokop, A. Stsiapanava, M. Kuty, I. Kuta-Smatanova, J. Dohnalek, P. Kulhanek, R. C. Wade, and J. Damborsky. Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations. Journal of Molecular Biology, 392(5):1339-1356, 2009.
9. T. Koudelakova, R. Chaloupkova, J. Brezovsky, Z. Prokop, E. Sebestova, M. Hesseler, M. Khabiri, M. Plevaka, D. Kulik, I. Kuta Smatanova, P. Rezacova, R. Ettrich, U. T. Bornscheuer, and J. Damborsky. Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel. Angewandte Chemie International Edition, 52(7), 2013.
10. B. Kozlikova, E. Sebestova, V. Sustr, J. Brezovsky, O. Strnad, L. Daniel, D. Bednar, A. Pavelka, M. Manak, M. Bezdeka, P. Benes, M. Kotry, A. W. Gora, J. Damborsky, and J. Sochor. CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. Bioinformatics, 30(18):2684-5, 2014.
11. M. Krone, M. Falk, S. Rehm, J. Pleiss, and T. Ertl. Interactive exploration of protein cavities. Computer Graphics Forum, 30(3):673-682, 2011.
12. O. D. Lampe, C. Correa, K.-L. Ma, and H. Hauser. Curve-centric volume reformation for comparative visualization. IEEE Transactions on Visualization and Computer Graphics, 15(6):1235-1242, 2009.
13. N. Lindow, D. Baum, A.-N. Bondar, and H.-C. Hege. Exploring cavity dynamics in biomolecular systems. BMC Bioinformatics, 14(S-19):S5, 2013.
14. N. Lindow, D. Baum, and H.-C. Hege. Voronoi-based extraction and visualization of molecular paths. IEEE Transactions on Visualization and Computer Graphics, 17(12):2025-2034, Dec 2011.
15. V. Liskova, D. Bednar, T. Prudnikova, P. Rezacova, T. Koudelakova, E. Sebestova, I. K. Smatanova, J. Brezovsky, R. Chaloupkova, and J. Damborsky. Balancing the stability-activity trade-off by fine-tuning dehalogenase access tunnels. ChemCatChem, 7(4):648-659, 2015.
16. P. Medek, P. Benes, and J. Sochor. Computation of tunnels in protein molecules using Delaunay triangulation. Journal of WSCG, 15(1-3):107-114, 2007.
17. J. Parulek, C. Turkay, N. Reuter, and I. Viola. Visual cavity analysis in molecular simulations. BMC Bioinformatics, 14(Suppl 19):S4, 2013.
18. M. Pavlova, M. Klvana, Z. Prokop, R. Chaloupkova, P. Banas, M. Otyepka, R. C. Wade, M. Tsuda, Y. Nagata, and J. Damborsky. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chemical Biology, 5:727-733, 2009.
19. M. Petrek, P. Kosinova, J. Koca, and M. Otyepka. MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure, 15(11):1357-1363, 2007.
20. M. Petrek, M. Otyepka, P. Banas, P. Kosinova, J. Koca, and J. Damborsky. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics, 7:316, 2006.
21. D. Sehnal, R. Svobodova Varekova, K. Berka, L. Pravda, V. Navratilova, P. Banas, C.-M. Ionescu, M. Otyepka, and J. Koca. MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics, 5(1), 2013.
22. J. Sykora, J. Brezovsky, T. Koudelakova, M. Lahoda, A. Fortova, T. Chernovets, R. Chaloupkova, V. Stepankova, Z. Prokop, I. K. Smatanova, M. Hof, and J. Damborsky. Dynamics and hydration explain failed functional transformation in dehalogenase design. Nat. Chem. Biol., 10(6):428-430, Jun 2014.
23. A. Vilanova Bartroli, R. Wegenkittl, A. König, and E. Gröller. Nonlinear virtual colon unfolding. In Visualization, 2001. VIS 2001. IEEE, pages 411-579, Oct 2001.
24. C. Ware. Information Visualization, Third Edition: Perception for Design. Elsevier, 2013.
25. E. Yaffe, D. Fishelovitch, H. J. Wolfson, D. Halperin, and R. Nussinov. MolAxis: Efficient and accurate identification of channels in macromolecules. Proteins: Structure, Function, and Bioinformatics, 73(1), 2008.