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Volumn 366, Issue 1878, 2008, Pages 3199-3219

Patient-specific simulation as a basis for clinical decision-making

Author keywords

Binding; Blood flow; HIV; Patient specific; Resistance; Urgent computing

Indexed keywords

ADMINISTRATIVE DATA PROCESSING; COMPUTER SYSTEMS; DECISION MAKING; DECISION SUPPORT SYSTEMS; HEALTH; HOSPITAL DATA PROCESSING; MANAGEMENT INFORMATION SYSTEMS; NUCLEIC ACIDS; ORGANIC ACIDS; PROBLEM SOLVING; WEIGHT CONTROL;

EID: 48349146758     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2008.0100     Document Type: Article
Times cited : (37)

References (43)
  • 1
    • 0032592496 scopus 로고    scopus 로고
    • UNICORE: Uniform access to supercomputing as an element of electronic commerce
    • doi:10.1016/S0167-739x(99)00007-2
    • Almond, J. & Snelling, D. 1999 UNICORE: uniform access to supercomputing as an element of electronic commerce. Future Generation Comput. Syst. 15, 539-548. (doi:10.1016/S0167-739x(99)00007-2)
    • (1999) Future Generation Comput. Syst , vol.15 , pp. 539-548
    • Almond, J.1    Snelling, D.2
  • 2
    • 32644449824 scopus 로고    scopus 로고
    • Mesoscopic simulations of systolic flow in the human abdominal aorta
    • doi:10.1016/j.jbiomech.2005.01.033
    • Artoli, A. M., Hoekstra, A. G. & Sloot, P. M. 2006 Mesoscopic simulations of systolic flow in the human abdominal aorta. J. Biomech. 39, 873-874. (doi:10.1016/j.jbiomech.2005.01.033)
    • (2006) J. Biomech , vol.39 , pp. 873-874
    • Artoli, A.M.1    Hoekstra, A.G.2    Sloot, P.M.3
  • 3
    • 0034352177 scopus 로고    scopus 로고
    • Strategies for the physiome project
    • doi:10.1114/1.1313771
    • Bassingthwaighte, J. B. 2000 Strategies for the physiome project. Ann. Biomed. Eng. 28, 1043-1058. (doi:10.1114/1.1313771)
    • (2000) Ann. Biomed. Eng , vol.28 , pp. 1043-1058
    • Bassingthwaighte, J.B.1
  • 5
    • 85020773040 scopus 로고    scopus 로고
    • 1 It could be argued that in a life-or-death situation, the processes needed to make a life-saving decision would take precedence over the issues of privacy and confidentiality.
    • 1 It could be argued that in a life-or-death situation, the processes needed to make a life-saving decision would take precedence over the issues of privacy and confidentiality.
  • 6
    • 0033988427 scopus 로고    scopus 로고
    • Hemodynamics in the carotid artery bifurcation: A comparison between numerical simulations and in vitro MRI measurements
    • doi:10.1016/S0021-9290(99)00164-5
    • Botnar, R., Rappitsch, G., Scheidegger, M. B., Liepsch, D., Perktold, K. & Boesiger, P. 2000 Hemodynamics in the carotid artery bifurcation: a comparison between numerical simulations and in vitro MRI measurements. J. Biomech. 33, 137-144. (doi:10.1016/S0021-9290(99)00164-5)
    • (2000) J. Biomech , vol.33 , pp. 137-144
    • Botnar, R.1    Rappitsch, G.2    Scheidegger, M.B.3    Liepsch, D.4    Perktold, K.5    Boesiger, P.6
  • 7
    • 33846822002 scopus 로고    scopus 로고
    • Ligand configurational entropy and protein binding
    • doi:10.1073/pnas.0610494104
    • Chang, C. A., Chen, W. & Gilson, M. K. 2007 Ligand configurational entropy and protein binding. Proc. Natl Acad. Sci. USA 104, 1534-1539. (doi:10.1073/pnas.0610494104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 1534-1539
    • Chang, C.A.1    Chen, W.2    Gilson, M.K.3
  • 9
    • 25144514551 scopus 로고    scopus 로고
    • Scientific grid computing
    • doi:10. 1098/rsta.2005.1632
    • Coveney, P. V. 2005 Scientific grid computing. Phil. Trans. R. Soc. A 363, 1707-1713. (doi:10. 1098/rsta.2005.1632)
    • (2005) Phil. Trans. R. Soc. A , vol.363 , pp. 1707-1713
    • Coveney, P.V.1
  • 10
    • 33044506498 scopus 로고    scopus 로고
    • Modelling biological complexity: A physical scientist's perspective
    • doi:10.1098/rsif.2005.0045
    • Coveney, P. V. & Fowler, P. W. 2005 Modelling biological complexity: a physical scientist's perspective. J. R. Soc. Interface 2, 267-280. (doi:10.1098/rsif.2005.0045)
    • (2005) J. R. Soc. Interface , vol.2 , pp. 267-280
    • Coveney, P.V.1    Fowler, P.W.2
  • 11
    • 33847221488 scopus 로고    scopus 로고
    • The application hosting environment: Lightweight middleware for grid-based computational science
    • doi:10.1016/j.cpc.2006.11.011
    • Coveney, P. V., Saksena, R. S., Zasada, S. J., McKeown, M. & Pickles, S. 2007 The application hosting environment: lightweight middleware for grid-based computational science. Comput. Phys. Commun. 176, 406-418. (doi:10.1016/j.cpc.2006.11.011)
    • (2007) Comput. Phys. Commun , vol.176 , pp. 406-418
    • Coveney, P.V.1    Saksena, R.S.2    Zasada, S.J.3    McKeown, M.4    Pickles, S.5
  • 12
    • 0030870159 scopus 로고    scopus 로고
    • Kinetic properties of saquinavir-resistant mutants of human immunodeficiency virus type 1 protease and their implications in drug resistance in vivo
    • doi:10.1021/bi971072e
    • Ermolieff, J., Lin, X. & Tang, J. 1997 Kinetic properties of saquinavir-resistant mutants of human immunodeficiency virus type 1 protease and their implications in drug resistance in vivo. Biochemistry 36, 12 364-12 370. (doi:10.1021/bi971072e)
    • (1997) Biochemistry , vol.36
    • Ermolieff, J.1    Lin, X.2    Tang, J.3
  • 13
    • 33744935671 scopus 로고    scopus 로고
    • Globus toolkit version 4: Software for service-oriented systems
    • Berlin, Germany: Springer
    • Foster, I. 2006 Globus toolkit version 4: software for service-oriented systems. In IFIP International Conference on Network and Parallel Computing, pp. 2-13. Berlin, Germany: Springer.
    • (2006) IFIP International Conference on Network and Parallel Computing , pp. 2-13
    • Foster, I.1
  • 15
    • 33744916260 scopus 로고    scopus 로고
    • The first functional demonstration of optical virtual concatenation as a technique for achieving terabit networking
    • doi:10.1016/j. future.2006.03.027
    • Hirano, A. et al. 2006 The first functional demonstration of optical virtual concatenation as a technique for achieving terabit networking. Future Generation Comput. Syst. 22, 876-883. (doi:10.1016/j. future.2006.03.027)
    • (2006) Future Generation Comput. Syst , vol.22 , pp. 876-883
    • Hirano, A.1
  • 17
    • 0035173377 scopus 로고    scopus 로고
    • Human immunodeficiency virus reverse transcriptase and protease sequence database: An expanded data model integrating natural language text and sequence analysis programs
    • doi:10.1093/nar/29.1.296
    • Kantor, R., Machekano, R., Gonzales, M. J., Dupnik, K., Schapiro, J. M. & Shafer, R. W. 2001 Human immunodeficiency virus reverse transcriptase and protease sequence database: an expanded data model integrating natural language text and sequence analysis programs. Nucleic Acids Res. 29, 296-299. (doi:10.1093/nar/29.1.296)
    • (2001) Nucleic Acids Res , vol.29 , pp. 296-299
    • Kantor, R.1    Machekano, R.2    Gonzales, M.J.3    Dupnik, K.4    Schapiro, J.M.5    Shafer, R.W.6
  • 18
    • 0742293840 scopus 로고    scopus 로고
    • MPICH-G2: A grid-enabled implementation of the message passing interface
    • doi:10.1016/S0743-7315(03)00002-9
    • Karonis, N. T., Toonen, B. & Foster, I. 2003 MPICH-G2: a grid-enabled implementation of the message passing interface. J. Parallel Distrib. Comput. 63, 551-563. (doi:10.1016/S0743-7315(03)00002-9)
    • (2003) J. Parallel Distrib. Comput , vol.63 , pp. 551-563
    • Karonis, N.T.1    Toonen, B.2    Foster, I.3
  • 19
    • 4544323776 scopus 로고    scopus 로고
    • Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations
    • doi:10.1002/prot.20192
    • Lepsik, M., Kriz, Z. & Havlas, Z. 2004 Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations. Proteins: Struct. Funct. Bioinform. 57, 279-293. (doi:10.1002/prot.20192)
    • (2004) Proteins: Struct. Funct. Bioinform , vol.57 , pp. 279-293
    • Lepsik, M.1    Kriz, Z.2    Havlas, Z.3
  • 20
    • 85020762242 scopus 로고    scopus 로고
    • MacLaren, J. 2007 HARC: the highly-available resource co-allocator. In Proc. GADA'07, LNCS 4804 (OTM Conferences 2007, Part II). Berlin, Germany: Springer.
    • MacLaren, J. 2007 HARC: the highly-available resource co-allocator. In Proc. GADA'07, LNCS 4804 (OTM Conferences 2007, Part II). Berlin, Germany: Springer.
  • 21
    • 48349094363 scopus 로고    scopus 로고
    • Life or death decision-making: The medical case for large-scale, on-demand grid computing
    • Manos, S., Zasada, S. & Coveney, P. V. 2008 Life or death decision-making: the medical case for large-scale, on-demand grid computing. CTWatch Q. J. 4, 35-45.
    • (2008) CTWatch Q. J , vol.4 , pp. 35-45
    • Manos, S.1    Zasada, S.2    Coveney, P.V.3
  • 22
    • 0030468331 scopus 로고    scopus 로고
    • Human immunodeficiency virus mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex
    • doi:10.1074/jbc.271.52.33231
    • Maschera, B., Darby, G., Palu, G., Wright, L. L., Tisdale, M., Myers, R., Blair, E. D. & Furfine, E. S. 1996 Human immunodeficiency virus mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex. J. Biol. Chem. 271, 33 231-33 235. (doi:10.1074/jbc.271.52.33231)
    • (1996) J. Biol. Chem , vol.271
    • Maschera, B.1    Darby, G.2    Palu, G.3    Wright, L.L.4    Tisdale, M.5    Myers, R.6    Blair, E.D.7    Furfine, E.S.8
  • 23
    • 44349177435 scopus 로고    scopus 로고
    • HemeLB: A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries
    • doi:10.1016/j.cpc.2008.02.013
    • Mazzeo, M. D. & Coveney, P. V. 2008 HemeLB: a high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries. Comput. Phys. Commun. 178, 894-914. (doi:10.1016/j.cpc.2008.02.013)
    • (2008) Comput. Phys. Commun , vol.178 , pp. 894-914
    • Mazzeo, M.D.1    Coveney, P.V.2
  • 24
    • 25144516750 scopus 로고    scopus 로고
    • A practical toolkit for computational steering
    • doi:10.1098/rsta.2005.1611
    • Pickles, S. M., Haines, R., Pinning, R. L. & Porter, A. R. 2005 A practical toolkit for computational steering. Phil. Trans. R. Soc. A 363, 1843-1853. (doi:10.1098/rsta.2005.1611)
    • (2005) Phil. Trans. R. Soc. A , vol.363 , pp. 1843-1853
    • Pickles, S.M.1    Haines, R.2    Pinning, R.L.3    Porter, A.R.4
  • 25
    • 39749115910 scopus 로고    scopus 로고
    • An automated molecular simulation-based binding affinity calculator for ligand-bound HIV-1 proteases
    • Preprint
    • Sadiq, S. K., Zasada, S. J., Wright, D., Stoica, I. & Coveney, P. V. 2008 An automated molecular simulation-based binding affinity calculator for ligand-bound HIV-1 proteases. Preprint.
    • (2008)
    • Sadiq, S.K.1    Zasada, S.J.2    Wright, D.3    Stoica, I.4    Coveney, P.V.5
  • 26
    • 0000342562 scopus 로고    scopus 로고
    • Mutations in retroviral genes associated with drug resistance
    • Schinazi, R. F., Larder, B. A. & Mellors, J. W. 1997 Mutations in retroviral genes associated with drug resistance. Antivir. News 5, 129-142.
    • (1997) Antivir. News , vol.5 , pp. 129-142
    • Schinazi, R.F.1    Larder, B.A.2    Mellors, J.W.3
  • 29
    • 22144494590 scopus 로고    scopus 로고
    • Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes
    • doi:10.1016/j.jviromet.2005.04.001
    • Snoek, J., Riva, C., Steegen, K., Schrooten, Y., Maes, B., Vergne, L., Van Laethem, K., Peeters, M. & Vandamme, A.-M. 2005 Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes. J. Virol. Methods 128, 47-53. (doi:10.1016/j.jviromet.2005.04.001)
    • (2005) J. Virol. Methods , vol.128 , pp. 47-53
    • Snoek, J.1    Riva, C.2    Steegen, K.3    Schrooten, Y.4    Maes, B.5    Vergne, L.6    Van Laethem, K.7    Peeters, M.8    Vandamme, A.-M.9
  • 30
    • 39749152456 scopus 로고    scopus 로고
    • Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
    • doi:10. 1021/ja0779250
    • Stoica, I., Sadiq, S. K. & Coveney, P. V. 2008 Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J. Am. Chem. Soc. 130, 2639-2648. (doi:10. 1021/ja0779250)
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 2639-2648
    • Stoica, I.1    Sadiq, S.K.2    Coveney, P.V.3
  • 32
    • 0003731910 scopus 로고    scopus 로고
    • Reducing risks, promoting healthy life. See http
    • The World Health Report 2002 Reducing risks, promoting healthy life. See http://www.who.int/ whr/en.
    • The World Health Report 2002
  • 33
    • 0029032769 scopus 로고
    • Pressure-induced arterial wall stress and atherosclerosis
    • doi:10.1016/0003-4975(94)01037-D
    • Thubrikar, M. J. & Robicsek, F. 1995 Pressure-induced arterial wall stress and atherosclerosis. Ann. Thoracic Surg. 59, 1594-1603. (doi:10.1016/0003-4975(94)01037-D)
    • (1995) Ann. Thoracic Surg , vol.59 , pp. 1594-1603
    • Thubrikar, M.J.1    Robicsek, F.2
  • 34
    • 0035876257 scopus 로고    scopus 로고
    • The binding energetics of first- and second-generation HIV-1 protease inhibitors: Implñications for drug design
    • doi:10.1006/abbi.2001.2333
    • Velazquez-Campoy, A., Kiso, Y. & Freire, E. 2001 The binding energetics of first- and second-generation HIV-1 protease inhibitors: implñications for drug design. Arch. Biochem. Biophys. 390, 169-175. (doi:10.1006/abbi.2001.2333)
    • (2001) Arch. Biochem. Biophys , vol.390 , pp. 169-175
    • Velazquez-Campoy, A.1    Kiso, Y.2    Freire, E.3
  • 36
    • 22544456941 scopus 로고    scopus 로고
    • Peptide recognition by the T cell receptor: Comparison of binding free energies from thermodynamic integration, poisson-Boltzmann and linear inberation energy approximations
    • doi:10.1098/ rsta.2005.1627
    • Wan, S., Coveney, P. V. & Flower, D. R. 2005 Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, poisson-Boltzmann and linear inberation energy approximations. Phil. Trans. R. Soc. A 363, 2037-2053. (doi:10.1098/ rsta.2005.1627)
    • (2005) Phil. Trans. R. Soc. A , vol.363 , pp. 2037-2053
    • Wan, S.1    Coveney, P.V.2    Flower, D.R.3
  • 37
    • 0035910029 scopus 로고    scopus 로고
    • Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
    • doi:10.1073/ pnas.251265598
    • Wang, W. & Kollman, P. A. 2001 Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proc. Natl Acad. Sci. USA 98, 14 937-14 942. (doi:10.1073/ pnas.251265598)
    • (2001) Proc. Natl Acad. Sci. USA , vol.98
    • Wang, W.1    Kollman, P.A.2
  • 38
    • 0034979318 scopus 로고    scopus 로고
    • Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
    • doi:10.1146/annurev.biophys.30.1.211
    • Wang, W., Donini, O., Reyes, C. M. & Kollman, P. A. 2001 Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomol. Struct. 30, 211-243. (doi:10.1146/annurev.biophys.30.1.211)
    • (2001) Annu. Rev. Biophys. Biomol. Struct , vol.30 , pp. 211-243
    • Wang, W.1    Donini, O.2    Reyes, C.M.3    Kollman, P.A.4
  • 39
    • 0027218692 scopus 로고
    • Structure-based inhibitors of HIV-1 protease
    • doi:10.1146/annurev.bi.62.070193.002551
    • Wlodawer, A. & Erickson, J. W. 1993 Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62, 543-585. (doi:10.1146/annurev.bi.62.070193.002551)
    • (1993) Annu. Rev. Biochem , vol.62 , pp. 543-585
    • Wlodawer, A.1    Erickson, J.W.2
  • 40
    • 20244387096 scopus 로고    scopus 로고
    • Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments
    • doi:10.1128/JVI.77.8.4836-4847.2003
    • Wu, T. D. et al. 2003 Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J. Virol. 77, 4836-4847. (doi:10.1128/JVI.77.8.4836-4847.2003)
    • (2003) J. Virol , vol.77 , pp. 4836-4847
    • Wu, T.D.1
  • 41
    • 33744934216 scopus 로고    scopus 로고
    • Co-scheduling with user-settable reservations
    • Job scheduling strategies for parallel processing eds D. G. Feitelson, E. Frachtenberg, L. Rudolph, & U. Schwiegelshohn, Berlin, Germany: Springer
    • Yoshimoto, K., Kovatch, P. & Andrews, P. 2005 Co-scheduling with user-settable reservations. In Job scheduling strategies for parallel processing (eds D. G. Feitelson, E. Frachtenberg, L. Rudolph, & U. Schwiegelshohn). Lecture Notes in Computer Sciences, no. 3834, pp. 146-156. Berlin, Germany: Springer.
    • (2005) Lecture Notes in Computer Sciences , vol.3834 , pp. 146-156
    • Yoshimoto, K.1    Kovatch, P.2    Andrews, P.3
  • 42
    • 0036298514 scopus 로고    scopus 로고
    • Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein flexibility
    • doi:10.1006/jmbi.2001.5173
    • Zoete, V., Michielin, O. & Karplus, M. 2002 Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J. Mol. Biol. 315, 21-52. (doi:10.1006/jmbi.2001.5173)
    • (2002) J. Mol. Biol , vol.315 , pp. 21-52
    • Zoete, V.1    Michielin, O.2    Karplus, M.3
  • 43
    • 27544505625 scopus 로고    scopus 로고
    • Bringing combined interaction to a problem solving environment for vascular reconstruction
    • doi:10.1016/j.future.2004. 04.004
    • Zudilova, E. V. & Sloot, P. M. A. 2005 Bringing combined interaction to a problem solving environment for vascular reconstruction. Future Generation Comput. Syst. 21, 1167-1176. (doi:10.1016/j.future.2004. 04.004)
    • (2005) Future Generation Comput. Syst , vol.21 , pp. 1167-1176
    • Zudilova, E.V.1    Sloot, P.M.A.2


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