CUDA accelerated molecular surface generation

Concurrency and Computation: Practice and Experience

Volumn 26, Issue 10, 2014, Pages 1819-1831

  D'Agostino, Daniele ^a   Clematis, Andrea ^a   Decherchi, Sergio ^b   Rocchia, Walter ^b   Milanesi, Luciano ^c   Merelli, Ivan ^c  

^a CNR   (Italy)

^b ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

^c INSTITUTE OF BIOMEDICAL TECHNOLOGIES   (Italy)

Author keywords

blobby molecular surface; CUDA molecular surface generation; GPU computing; Richards Connolly molecular surface; solvent accessible molecular surface; van der Waals molecular surface

Indexed keywords

BOLTZMANN EQUATION; MOLECULAR DYNAMICS; POISSON EQUATION; SOLVENTS; VAN DER WAALS FORCES; VISUALIZATION;

DIRECT VISUALIZATION; GPU COMPUTING; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SURFACE GENERATIONS; MOLECULAR SURFACES; POISSON-BOLTZMANN EQUATIONS; SURFACE RESOLUTION; VISUALIZATION PIPELINE;

PIPELINE PROCESSING SYSTEMS;

EID: 84902553505     PISSN: 15320626     EISSN: 15320634     Source Type: Journal    
DOI: 10.1002/cpe.3120     Document Type: Conference Paper

References (34)

1. Yu Z, Hols MJ, Cheng Y, McCammon JA,. Feature-preserving adaptive mesh generation for molecular shape modelling and simulation. Journal of Molecular Graphics and Modelling 2008; 26 (8): 1370-1380. DOI: 10.1016/j.jmgm.2008.01.007.
2. Chavent M, Levy B, Maigret B,. MetaMol: high-quality visualization of molecular skin surface. Journal of Molecular Graphics and Modelling 2008; 27 (2): 209-216. DOI: 10.1016/j.jmgm.2008.04.007.
3. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJE, Vajda S, Vakser I, Wodak SJ,. CAPRI: a critical assessment of predicted interactions. Proteins: Structure, Function, and Genetics 2003; 52: 2-9. DOI: 10.1002/prot.10381.
4. Via A, Ferre F, Brannetti B, Helmer-Citterich M,. Protein surface similarities: a survey of methods to describe and compare protein surfaces. Cellular and Molecular Life Sciences 2000; 57: 1970-1977.
5. D'Agostino D, Decherchi S, Galizia A, Colmenares J, Quarati A, Rocchia W, Clematis A,. CUDA accelerated blobby molecular surface generation. Proceedings of the 9th International Conference on Parallel Processing and Applied Mathematics (Lecture Notes in Computer Science), 2012; 347-356, DOI: 10.1007/978-3-642-31464-3-35.
6. D'Agostino D, Merelli I, Clematis A, Milanesi L, Orro A,. A parallel workflow for the reconstruction of molecular surfaces. Parallel Computing: Architectures, Algorithms and Applications, Advances in Parallel Computing 2008; 15: 147-154.
7. Decherchi S, Rocchia W,. A general and robust ray casting based algorithm for triangulating surfaces at the nanoscale. PLoS ONE 2013; 8 (4): e59744. DOI: 10.1371/journal.pone.0059744.
8. Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, Weissig H, Westbrook J,. The Protein Data Bank and the challenge of structural genomics. Nature Structural Biology 2000; 7 (11): 957-959.
9. Akkiraju N, Edelsbrunner H, Facello M, Fu P, Mucke EP, Varela C,. Alpha shapes: definition and software. Proceedings of the 1st International Computational Geometry Software Workshop 1995: 63-66.
10. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B,. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. Journal of Computational Chemistry 2001; 23 (1): 128-137.
11. Zhang Y, Xu G, Bajaj C,. Quality meshing of implicit solvation models of biomolecular structures. (Journal Computer Aided Geometric Design Special Issue: Applications of Geometric Modelling in the Life Sciences) 2006; 23 (6): 510-530. DOI: 10.1016/j.cagd.2006.01.008.
12. Connolly ML,. The molecular surface package. Journal of Molecular Graphics 1993; 11 (2): 139-141. DOI: 10.1016/0263-7855(93)87010-3.
13. Sanner M, Olson AJ, Spehner JC,. Fast and robust computation of molecular surfaces. Proceedings of the 11th Annual Symposium on Computational Geometry (ACG '95) 1995: 406-407, ACM New York, NY, USA. DOI: 10.1145/220279.220324.
14. Vorobjev YN, Hermans J,. SIMS: computation of a smooth invariant molecular surface. Biophysical Journal 1997; 73: 722-732. DOI: 10.1016/S0006-3495(97)78105-0.
15. Connolly ML,. Solvent-accessible surfaces of proteins and nucleicacids. Science 1983; 221: 709-713.
16. Lee B, Richards FM,. The interpretation of protein structures: estimation of static accessibility. Journal of Molecular Biology 1971; 55: 379-400.
17. Blinn J,. A generalization of algebraic surface drawing. ACM Transactions on Graphics 1982; 1 ((3)): 235256.
18. Decherchi S, Colmenares J, Catalano CE, Spagnuolo M, Alexov E, Rocchia W,. Between algorithm and model, different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution. Communications in Computational Physics 2013; 13 (1): 61-89.
19. Vakser IA, Matar OG, Lam CF,. A systematic study of low-resolution recognition in protein-protein complexes. Proceedings of the National Academy of Sciences 1999; 96: 8477-8482.
20. Sanner M, Olson AJ, Spehner JC,. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996; 38 ((3)): 305-320. DOI: 10.1002/(SICI)1097-0282(199603)38:3.
21. Nicholls A, Sharp KA, Honig B,. Protein folding and association, insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Structure, Function, and Genetics 1991; 11: 281-296. DOI: 10.1002/prot. 340110407.
22. The PyMOL molecular graphics system, 2013. (Available from: http://www.pymol.org) Accessed 7 Aug 2013.
23. Bohm HJ,. Towards the automatic design of synthetically accessible protein ligands: peptides, amides and peptidomimetics. Journal of Computer-Aided Molecular Design 1996; 4: 265-272. DOI: 10.1007/BF00124496.
24. Stone JE, Kohlmeyer A, Vandivort KL, Schulten K,. Immersive molecular visualization and interactive modeling with commodity hardware. Advances in Visual Computing (Lecture Notes in Computer Science) 2010; 6454: 382-393. DOI: 10.1007/978-3-642-17274-8-38.
25. Stone JE, Hardy DJ, Ufimtsev IS, Schulten K,. GPU-accelerated molecular modeling coming of age. Journal of Molecular Graphics and Modelling 2010; 29: 116-125. DOI: 10.1016/j.jmgm.2010.06.010.
26. Chavent M, Levy B, Krone M, Bidmon K, Nomine JP, Ertl T, Baaden M,. GPU-powered tools boost molecular visualization. Brief Bioinform 2011; 12 (6): 689-701. DOI: 10.1093/bib/bbq089.
27. Chavent M, Vanel A, Tek A, Levy B, Robert S, Raffin B, Baaden M,. GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids. Journal of Computational Chemistry 2011; 32 (13): 2924-35. DOI: 10.1002/jcc.21861.
28. Lindow N, Baum D, Prohaska S, Hege HC,. Accelerated visualization of dynamic molecular surfaces. Eurographics/ IEEE-VGTC Symposium on Visualization 2010; 29 (3): 943-952. DOI: 10.1111/j.1467-8659.2009.01693.x.
29. Byungjoo K, Ku-Jin K, Joon-Kyung S,. GPU accelerated molecular surface computing. Applied Mathematics and Information Sciences 2012; 6 ((1S)): 185S-194S.
30. Dias S, Bora K, Gomes A,. CUDA-based triangulations of convolution molecular surfaces, Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing (HPDC '10), 2010; 531-540, ACM, New York, http://www.acm.org/about/contact-us/. DOI: 10.1145/1851476.1851553.
31. Lorensen WE, Cline HE,. Marching cubes: a high resolution 3-D surface construction algorithm. Computer Graphics 1987; 21 (3): 163-169. DOI: 10.1145/37402.37422.
32. D'Agostino D, Seinstra FJ,. An efficient isosurface extraction component for visualization pipelines based on the CUDA architecture. Technical Report IR-CS-64-2010, Vrije Universiteit, Amsterdam, The Netherlands, 2010.
33. Watt A, Watt M,. Advanced Animation and Rendering Techniques Theory and Practice. Addison-Wesley/ACM Press: New York, New York, 1992.
34. D'Agostino D, Clematis A, Gianuzzi V,. Parallel isosurface extraction for 3D data analysis workflows in distributed environments. Concurrency and Computation: Practice and Experience 2011; 23 (11): 1284-1310. DOI: 10.1002/cpe.1710.