Parallel, stochastic measurement of molecular surface area
Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorith...
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| Veröffentlicht in: | Journal of molecular graphics & modelling Jg. 27; H. 1; S. 82 - 87 |
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| Format: | Journal Article |
| Sprache: | Englisch |
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01.08.2008
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| ISSN: | 1093-3263, 1873-4243, 1873-4243 |
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| Abstract | Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited.
We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering.
We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy. |
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| AbstractList | Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited.
We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering.
We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy. Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited. We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering. We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy. Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited. We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering. We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy.Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited. We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering. We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy. |
| Author | Juba, Derek Varshney, Amitabh |
| Author_xml | – sequence: 1 givenname: Derek surname: Juba fullname: Juba, Derek email: juba@cs.umd.edu – sequence: 2 givenname: Amitabh surname: Varshney fullname: Varshney, Amitabh email: varshney@cs.umd.edu |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/18424205$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_1016_j_jmgm_2010_06_010 crossref_primary_10_1186_1471_2105_14_S4_S4 crossref_primary_10_1016_j_jcp_2010_01_004 crossref_primary_10_1088_1749_4699_6_1_015007 crossref_primary_10_1007_s10509_018_3265_6 crossref_primary_10_1371_journal_pone_0059744 crossref_primary_10_1016_j_patcog_2010_06_002 crossref_primary_10_1080_07391102_2010_10507359 crossref_primary_10_1007_s00244_015_0236_6 |
| Cites_doi | 10.1016/j.cad.2005.07.002 10.1126/science.6879170 10.1145/146382.146385 10.1107/S0021889883010985 10.1016/j.jmb.2006.05.023 10.1073/pnas.77.4.1736 10.1109/TVCG.2007.70517 10.1016/j.jmgm.2006.02.012 10.1145/357306.357310 10.1145/1185657.1185660 10.1146/annurev.bb.06.060177.001055 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H 10.1145/174462.156635 10.1109/38.310720 10.1002/prot.10379 10.1016/0022-2836(71)90324-X 10.1016/S0010-4485(02)00100-8 10.1002/(SICI)1096-987X(199802)19:3<319::AID-JCC6>3.0.CO;2-W 10.1021/j100011a016 10.1093/nar/28.1.235 |
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| References | Sanner, Olson, Spehner (bib5) 1995 Fraczkiewicz, Braun (bib6) 1998; 19 Liu, Yong, Zhang, Yan, Sun (bib23) 2006; 38 Rovira, Wonka, Castro, Sbert (bib27) 2005 Bratley, Fox, Niederreiter (bib25) 1992; 2 Varshney, Brooks, Wright (bib17) 1994; 14 Grant, Pickup (bib19) 1995; 99 Lee, Richards (bib13) 1971; 55 Kreylos, Max, Hamann, Crivelli, Bethel (bib1) 2003 (bib29) 2007 E.W. Weisstein, Sphere Point Picking, From MathWorld—A Wolfram Web Resource Liang, Edelsbrunner, Fu, Sudhakar, Subramaniam (bib31) 1998; 33 Gärtner (bib28) 1999 Edelbrunner, Muecke (bib15) 1994; 13 Richards (bib14) 1977; 6 Ritchie (bib20) 2003; 52 Connolly (bib4) 1983; 221 Connolly (bib3) 1983; 16 Li, Wang, Bowyer (bib22) 2003; 35 Can, Chen, Wang (bib7) 2006; 25 . Wodak, Janin (bib16) 1980; 77 Voss, Gerstein, Steitz, Moore (bib8) 2006; 360 C. Bajaj, V. Siddavanahalli, An adaptive grid based method for computing molecular surfaces and properties, Technical Report tr06–56, University of Texas, 2006. Berman, Westbrook, Feng, Gilliland, Bhat, Weissig, Shindyalov, Bourne (bib21) 2000; 28 O.D. Lampe, I. Viola, N. Reuter, H. Hauser, Two level approach to efficient visualization of protein dynamics, in: Proceedings of IEEE Visualization. 13 (6) (2007) 1616–1623. GNU Scientific Library Blinn (bib18) 1982; 1 P. Schröder, What can we measure? in: SIGGRAPH ’06: ACM SIGGRAPH 2006 Courses, ACM Press, New York, NY, USA, 2006, pp. 5–9. Bajaj, Djeu, Siddavanahalli, Thane (bib10) 2004 10.1016/j.jmgm.2008.03.001_bib9 Varshney (10.1016/j.jmgm.2008.03.001_bib17) 1994; 14 Bratley (10.1016/j.jmgm.2008.03.001_bib25) 1992; 2 Rovira (10.1016/j.jmgm.2008.03.001_bib27) 2005 10.1016/j.jmgm.2008.03.001_bib30 10.1016/j.jmgm.2008.03.001_bib11 Connolly (10.1016/j.jmgm.2008.03.001_bib3) 1983; 16 10.1016/j.jmgm.2008.03.001_bib12 Liu (10.1016/j.jmgm.2008.03.001_bib23) 2006; 38 Wodak (10.1016/j.jmgm.2008.03.001_bib16) 1980; 77 10.1016/j.jmgm.2008.03.001_bib2 Sanner (10.1016/j.jmgm.2008.03.001_bib5) 1995 Grant (10.1016/j.jmgm.2008.03.001_bib19) 1995; 99 Li (10.1016/j.jmgm.2008.03.001_bib22) 2003; 35 Gärtner (10.1016/j.jmgm.2008.03.001_bib28) 1999 10.1016/j.jmgm.2008.03.001_bib26 Kreylos (10.1016/j.jmgm.2008.03.001_bib1) 2003 Connolly (10.1016/j.jmgm.2008.03.001_bib4) 1983; 221 Berman (10.1016/j.jmgm.2008.03.001_bib21) 2000; 28 Voss (10.1016/j.jmgm.2008.03.001_bib8) 2006; 360 Ritchie (10.1016/j.jmgm.2008.03.001_bib20) 2003; 52 Bajaj (10.1016/j.jmgm.2008.03.001_bib10) 2004 10.1016/j.jmgm.2008.03.001_bib24 Blinn (10.1016/j.jmgm.2008.03.001_bib18) 1982; 1 Liang (10.1016/j.jmgm.2008.03.001_bib31) 1998; 33 Lee (10.1016/j.jmgm.2008.03.001_bib13) 1971; 55 Edelbrunner (10.1016/j.jmgm.2008.03.001_bib15) 1994; 13 (10.1016/j.jmgm.2008.03.001_bib29) 2007 Can (10.1016/j.jmgm.2008.03.001_bib7) 2006; 25 Fraczkiewicz (10.1016/j.jmgm.2008.03.001_bib6) 1998; 19 Richards (10.1016/j.jmgm.2008.03.001_bib14) 1977; 6 |
| References_xml | – start-page: 406 year: 1995 end-page: 407 ident: bib5 article-title: Fast and robust computation of molecular surfaces publication-title: SCG ’95: Proceedings of the Eleventh Annual Symposium on Computational Geometry – start-page: 243 year: 2004 end-page: 250 ident: bib10 article-title: TexMol: interactive visual exploration of large flexible multi-component molecular complexes publication-title: VIS ’04: Proceedings of the Conference on Visualization ’04 – volume: 1 start-page: 235 year: 1982 end-page: 256 ident: bib18 article-title: A generalization of algebraic surface drawing publication-title: ACM Trans. Graphic. – reference: C. Bajaj, V. Siddavanahalli, An adaptive grid based method for computing molecular surfaces and properties, Technical Report tr06–56, University of Texas, 2006. – start-page: 581 year: 2003 end-page: 588 ident: bib1 article-title: Interactive protein manipulation publication-title: Proceedings of IEEE Visualization – volume: 55 start-page: 379 year: 1971 end-page: 400 ident: bib13 article-title: The interpretation of protein structures: estimation of static accessibility publication-title: J. Mol. Biol. – reference: GNU Scientific Library, – year: 2007 ident: bib29 publication-title: Point-Based Graphics – volume: 77 start-page: 1736 year: 1980 end-page: 1740 ident: bib16 article-title: Analytical approximation to the accessible surface area of proteins publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 2 start-page: 195 year: 1992 end-page: 213 ident: bib25 article-title: Implementation and tests of low-discrepancy sequences publication-title: ACM Trans. Model. Comput. Simul. – reference: O.D. Lampe, I. Viola, N. Reuter, H. Hauser, Two level approach to efficient visualization of protein dynamics, in: Proceedings of IEEE Visualization. 13 (6) (2007) 1616–1623. – volume: 360 start-page: 893 year: 2006 end-page: 906 ident: bib8 article-title: The geometry of the ribosomal polypeptide exit tunnel publication-title: J. Mol. Biol. – volume: 221 start-page: 709 year: 1983 ident: bib4 article-title: Solvent-accessible surfaces of proteins and nucleic acids publication-title: Science – volume: 35 start-page: 771 year: 2003 end-page: 782 ident: bib22 article-title: Using low-discrepency sequences and the Crofton formula to compute surface areas of geometric models publication-title: Comput. Aided Des. – start-page: 109 year: 2005 end-page: 118 ident: bib27 article-title: Point Sampling with Uniformly Distributed Lines, Point-Based Graphics, 2005 publication-title: Eurographics/IEEE VGTC Symposium Proceedings – volume: 14 start-page: 19 year: 1994 end-page: 25 ident: bib17 article-title: Linearly scalable computation of smooth molecular surfaces publication-title: IEEE Comput. Graphic. Appl. – reference: P. Schröder, What can we measure? in: SIGGRAPH ’06: ACM SIGGRAPH 2006 Courses, ACM Press, New York, NY, USA, 2006, pp. 5–9. – volume: 33 start-page: 18 year: 1998 end-page: 29 ident: bib31 article-title: Analytical shape computation of macromolecules. II. Inaccessible cavities in proteins publication-title: Proteins Struct. Funct. Genet. – reference: E.W. Weisstein, Sphere Point Picking, From MathWorld—A Wolfram Web Resource, – volume: 38 start-page: 55 year: 2006 end-page: 68 ident: bib23 article-title: A quasi-Monte Carlo method for computing areas of point-sampled surfaces publication-title: Comput. Aided Des. – volume: 16 start-page: 548 year: 1983 end-page: 558 ident: bib3 article-title: Analytical molecular surface calculation publication-title: J. Appl. Crystallogr. – volume: 52 start-page: 98 year: 2003 end-page: 106 ident: bib20 article-title: Evaluation of protein docking predictions using hex 3.1 in capri rounds 1 and 2 publication-title: Proteins: Struct., Funct. Genet. – volume: 25 start-page: 442 year: 2006 end-page: 454 ident: bib7 article-title: Efficient molecular surface generation using level-set methods publication-title: J. Mol. Graph. Model – volume: 13 start-page: 43 year: 1994 end-page: 72 ident: bib15 article-title: Three-dimensional alpha shapes publication-title: ACM Trans. Graphic. – start-page: 325 year: 1999 end-page: 338 ident: bib28 article-title: Fast and robust smallest enclosing balls publication-title: ESA ’99: Proceedings of the 7th Annual European Symposium on Algorithms – volume: 28 start-page: 235 year: 2000 end-page: 242 ident: bib21 article-title: The Protein Data Bank publication-title: Nucleic Acids Res. – volume: 19 start-page: 319 year: 1998 end-page: 333 ident: bib6 article-title: Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules publication-title: J. Comput. Chem. – volume: 6 start-page: 151 year: 1977 end-page: 176 ident: bib14 article-title: Areas, volumes, packing, and protein structure publication-title: Ann. Rev. Biophys. Bioeng. – reference: . – volume: 99 start-page: 3503 year: 1995 end-page: 3510 ident: bib19 article-title: A Gaussian description of molecular shape publication-title: J. Phys. Chem. – volume: 38 start-page: 55 issue: 1 year: 2006 ident: 10.1016/j.jmgm.2008.03.001_bib23 article-title: A quasi-Monte Carlo method for computing areas of point-sampled surfaces publication-title: Comput. Aided Des. doi: 10.1016/j.cad.2005.07.002 – start-page: 406 year: 1995 ident: 10.1016/j.jmgm.2008.03.001_bib5 article-title: Fast and robust computation of molecular surfaces – ident: 10.1016/j.jmgm.2008.03.001_bib26 – volume: 221 start-page: 709 issue: 4612 year: 1983 ident: 10.1016/j.jmgm.2008.03.001_bib4 article-title: Solvent-accessible surfaces of proteins and nucleic acids publication-title: Science doi: 10.1126/science.6879170 – ident: 10.1016/j.jmgm.2008.03.001_bib24 – volume: 2 start-page: 195 issue: 3 year: 1992 ident: 10.1016/j.jmgm.2008.03.001_bib25 article-title: Implementation and tests of low-discrepancy sequences publication-title: ACM Trans. Model. Comput. Simul. doi: 10.1145/146382.146385 – volume: 16 start-page: 548 issue: 5 year: 1983 ident: 10.1016/j.jmgm.2008.03.001_bib3 article-title: Analytical molecular surface calculation publication-title: J. Appl. Crystallogr. doi: 10.1107/S0021889883010985 – volume: 360 start-page: 893 issue: 4 year: 2006 ident: 10.1016/j.jmgm.2008.03.001_bib8 article-title: The geometry of the ribosomal polypeptide exit tunnel publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2006.05.023 – ident: 10.1016/j.jmgm.2008.03.001_bib11 – volume: 77 start-page: 1736 issue: 4 year: 1980 ident: 10.1016/j.jmgm.2008.03.001_bib16 article-title: Analytical approximation to the accessible surface area of proteins publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.77.4.1736 – ident: 10.1016/j.jmgm.2008.03.001_bib2 doi: 10.1109/TVCG.2007.70517 – volume: 25 start-page: 442 issue: 4 year: 2006 ident: 10.1016/j.jmgm.2008.03.001_bib7 article-title: Efficient molecular surface generation using level-set methods publication-title: J. Mol. Graph. Model doi: 10.1016/j.jmgm.2006.02.012 – volume: 1 start-page: 235 issue: 3 year: 1982 ident: 10.1016/j.jmgm.2008.03.001_bib18 article-title: A generalization of algebraic surface drawing publication-title: ACM Trans. Graphic. doi: 10.1145/357306.357310 – start-page: 243 year: 2004 ident: 10.1016/j.jmgm.2008.03.001_bib10 article-title: TexMol: interactive visual exploration of large flexible multi-component molecular complexes – ident: 10.1016/j.jmgm.2008.03.001_bib9 – ident: 10.1016/j.jmgm.2008.03.001_bib30 doi: 10.1145/1185657.1185660 – start-page: 581 year: 2003 ident: 10.1016/j.jmgm.2008.03.001_bib1 article-title: Interactive protein manipulation – volume: 6 start-page: 151 issue: 1 year: 1977 ident: 10.1016/j.jmgm.2008.03.001_bib14 article-title: Areas, volumes, packing, and protein structure publication-title: Ann. Rev. Biophys. Bioeng. doi: 10.1146/annurev.bb.06.060177.001055 – volume: 33 start-page: 18 issue: 1 year: 1998 ident: 10.1016/j.jmgm.2008.03.001_bib31 article-title: Analytical shape computation of macromolecules. II. Inaccessible cavities in proteins publication-title: Proteins Struct. Funct. Genet. doi: 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H – start-page: 325 year: 1999 ident: 10.1016/j.jmgm.2008.03.001_bib28 article-title: Fast and robust smallest enclosing balls – volume: 13 start-page: 43 year: 1994 ident: 10.1016/j.jmgm.2008.03.001_bib15 article-title: Three-dimensional alpha shapes publication-title: ACM Trans. Graphic. doi: 10.1145/174462.156635 – volume: 14 start-page: 19 issue: 5 year: 1994 ident: 10.1016/j.jmgm.2008.03.001_bib17 article-title: Linearly scalable computation of smooth molecular surfaces publication-title: IEEE Comput. Graphic. Appl. doi: 10.1109/38.310720 – volume: 52 start-page: 98 issue: 1 year: 2003 ident: 10.1016/j.jmgm.2008.03.001_bib20 article-title: Evaluation of protein docking predictions using hex 3.1 in capri rounds 1 and 2 publication-title: Proteins: Struct., Funct. Genet. doi: 10.1002/prot.10379 – start-page: 109 year: 2005 ident: 10.1016/j.jmgm.2008.03.001_bib27 article-title: Point Sampling with Uniformly Distributed Lines, Point-Based Graphics, 2005 – volume: 55 start-page: 379 issue: 3 year: 1971 ident: 10.1016/j.jmgm.2008.03.001_bib13 article-title: The interpretation of protein structures: estimation of static accessibility publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(71)90324-X – ident: 10.1016/j.jmgm.2008.03.001_bib12 – year: 2007 ident: 10.1016/j.jmgm.2008.03.001_bib29 – volume: 35 start-page: 771 issue: 9 year: 2003 ident: 10.1016/j.jmgm.2008.03.001_bib22 article-title: Using low-discrepency sequences and the Crofton formula to compute surface areas of geometric models publication-title: Comput. Aided Des. doi: 10.1016/S0010-4485(02)00100-8 – volume: 19 start-page: 319 issue: 3 year: 1998 ident: 10.1016/j.jmgm.2008.03.001_bib6 article-title: Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules publication-title: J. Comput. Chem. doi: 10.1002/(SICI)1096-987X(199802)19:3<319::AID-JCC6>3.0.CO;2-W – volume: 99 start-page: 3503 issue: 11 year: 1995 ident: 10.1016/j.jmgm.2008.03.001_bib19 article-title: A Gaussian description of molecular shape publication-title: J. Phys. Chem. doi: 10.1021/j100011a016 – volume: 28 start-page: 235 year: 2000 ident: 10.1016/j.jmgm.2008.03.001_bib21 article-title: The Protein Data Bank publication-title: Nucleic Acids Res. doi: 10.1093/nar/28.1.235 |
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| SubjectTerms | Algorithms Databases, Protein GPU Models, Molecular Molecular surface Parallel Progressive Proteins - chemistry Quasi-random Stochastic Stochastic Processes Surface Properties Time Factors |
| Title | Parallel, stochastic measurement of molecular surface area |
| URI | https://dx.doi.org/10.1016/j.jmgm.2008.03.001 https://www.ncbi.nlm.nih.gov/pubmed/18424205 https://www.proquest.com/docview/69465510 |
| Volume | 27 |
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