메뉴 건너뛰기




Volumn , Issue , 2010, Pages

GPU-Accelerated multi-scoring functions protein loop structure sampling

Author keywords

GPU programming; Protein structure modeling; Sampling

Indexed keywords

BACKBONE STRUCTURES; COMPUTATIONAL RESULTS; GPU PROGRAMMING; LARGE POPULATION; LOOP STRUCTURE; PROTEIN STRUCTURE MODELING; PROTEIN STRUCTURES; ROOT MEAN SQUARE DEVIATIONS; SAMPLING PROCESS; SCORING FUNCTIONS; TORSION ANGLE; VAN DER WAALS;

EID: 77954071718     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPSW.2010.5470901     Document Type: Conference Paper
Times cited : (3)

References (29)
  • 1
    • 0034567501 scopus 로고    scopus 로고
    • Ab initio loop modeling and its application to homology modeling
    • R. E. Bruccoleri, "Ab initio loop modeling and its application to homology modeling," Methods in Molecular Biology, 143: 247-264, 2000.
    • (2000) Methods in Molecular Biology , vol.143 , pp. 247-264
    • Bruccoleri, R.E.1
  • 2
    • 34748913195 scopus 로고    scopus 로고
    • The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c
    • O. Y. Dmitriev, R. H. Fillingame, "The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c," Protein Science, 16(10): 2118-2122, 2007.
    • (2007) Protein Science , vol.16 , Issue.10 , pp. 2118-2122
    • Dmitriev, O.Y.1    Fillingame, R.H.2
  • 3
    • 0024310232 scopus 로고
    • Modeling antibody hypervariable loops: A combined algorithm
    • A. C. Martin, J. C. Cheetham, A. R. Rees, "Modeling antibody hypervariable loops: a combined algorithm," PNAS, 86(23): 9268- 9272, 1989.
    • (1989) PNAS , vol.86 , Issue.23 , pp. 9268-9272
    • Martin, A.C.1    Cheetham, J.C.2    Rees, A.R.3
  • 4
    • 26944443142 scopus 로고    scopus 로고
    • Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels
    • A. Tasneem, L. M. Iyer, E. Jakobsson, E., L. Aravind, "Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels," Genome Biol., 6(1) R4, 2005.
    • (2005) Genome Biol. , vol.6 , Issue.1
    • Tasneem, A.1    Iyer, L.M.2    Jakobsson, E.E.3    Aravind, L.4
  • 5
    • 33646550515 scopus 로고    scopus 로고
    • Voltage sensor conformations in the open and closed states in Rosetta structural models of K+ channels
    • V. Yarov-Yarovoy, D. Baker, W.A. Catterall, "Voltage sensor conformations in the open and closed states in ROSETTA structural models of K+ channels," PNAS, 103: 7292-7297, 2006.
    • (2006) PNAS , vol.103 , pp. 7292-7297
    • Yarov-Yarovoy, V.1    Baker, D.2    Catterall, W.A.3
  • 7
    • 77954042859 scopus 로고    scopus 로고
    • Backbone statistical potential from local sequence-structure interactions in protein loops
    • in press
    • I. Rata, Y. Li, E. Jakobsson, "Backbone statistical potential from local sequence-structure interactions in protein loops," in press, Journal of Phys. Chem. B. 2009.
    • (2009) Journal of Phys. Chem. B
    • Rata, I.1    Li, Y.2    Jakobsson, E.3
  • 8
    • 0031021792 scopus 로고    scopus 로고
    • A fast and efficient program for modeling protein loops
    • H. Zhang, L. Lai, Y. Han, Y. Tang, "A Fast and Efficient Program for Modeling Protein Loops," Biopolymers, 41: 61-72, 1997.
    • (1997) Biopolymers , vol.41 , pp. 61-72
    • Zhang, H.1    Lai, L.2    Han, Y.3    Tang, Y.4
  • 9
    • 27344445735 scopus 로고    scopus 로고
    • Effective and efficient algorithm for multiobjective optimization of hyrdologic models
    • J. A. Vrugt, H. V. Gupta, L. A. Bastidas, W. Boutem, S. Sorooshian, "Effective and Efficient Algorithm for Multiobjective Optimization of Hyrdologic Models," Water Resources Research, 39(8): 1214-1232, 2002.
    • (2002) Water Resources Research , vol.39 , Issue.8 , pp. 1214-1232
    • Vrugt, J.A.1    Gupta, H.V.2    Bastidas, L.A.3    Boutem, W.4    Sorooshian, S.5
  • 10
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • C. B. Anfinsen, "Principles that Govern the Folding of Protein Chains," Science, 181: 223-230, 1973.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 11
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with rosetta
    • C. A. Rohl, C. E. Strauss, D. Chivian, D. Baker, "Modeling structurally variable regions in homologous proteins with rosetta," Proteins, 55:656-677, 2004.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.2    Chivian, D.3    Baker, D.4
  • 13
    • 1642575364 scopus 로고    scopus 로고
    • Accurate and efficient loop selections using DFIRE-based all-atom statistical potential
    • C. Zhang, S. Liu, Y. Zhou, "Accurate and efficient loop selections using DFIRE-based all-atom statistical potential," Protein Science, 13: 391-399, 2004.
    • (2004) Protein Science , vol.13 , pp. 391-399
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 14
    • 58149157667 scopus 로고    scopus 로고
    • Prediction of protein loop conformations using the AGBNP implicit solvent model and torsion angle sampling
    • A. K. Felts, E. Gallicchio, D. Chekmarev, K. A. Paris, R. A. Friesner, R. M. Levy, "Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling," J. Chem. Theory Comput., 4(5): 855-868, 2008.
    • (2008) J. Chem. Theory Comput. , vol.4 , Issue.5 , pp. 855-868
    • Felts, A.K.1    Gallicchio, E.2    Chekmarev, D.3    Paris, K.A.4    Friesner, R.A.5    Levy, R.M.6
  • 15
    • 0032612579 scopus 로고    scopus 로고
    • Ab initio protein structure prediction of CASP III targets using Rosetta
    • K. T. Simons, R. Bonneau, I. Ruczinski, and D. Baker, "Ab initio Protein Structure Prediction of CASP III Targets Using ROSETTA," Proteins, 37(3): 171-176, 1999.
    • (1999) Proteins , vol.37 , Issue.3 , pp. 171-176
    • Simons, K.T.1    Bonneau, R.2    Ruczinski, I.3    Baker, D.4
  • 16
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • W. L. Jorgensen, D. S. Maxwell, J. Tirado-Rives, "Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids," J. Am. Chem. Soc., 118: 11225-11236, 1996.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 17
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • H. Zhou, Y. Zhou, "Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction," Protein Science, 11: 2714-2726, 2002.
    • (2002) Protein Science , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 18
    • 1442330396 scopus 로고    scopus 로고
    • AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and highresolution modeling
    • E. Gallicchio, R. M. Levy, "AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and highresolution modeling," J. Comput. Chem., 25(4): 479-499, 2004.
    • (2004) J. Comput. Chem. , vol.25 , Issue.4 , pp. 479-499
    • Gallicchio, E.1    Levy, R.M.2
  • 19
    • 56449101788 scopus 로고    scopus 로고
    • Investigations into the effect of multiobjectivization in protein structure prediction
    • J. Handl, S. C. Lovell, J. Knowles, "Investigations into the Effect of Multiobjectivization in Protein Structure Prediction," Lecture Notes in Computer Science, 5199: 702-711, 2008.
    • (2008) Lecture Notes in Computer Science , vol.5199 , pp. 702-711
    • Handl, J.1    Lovell, S.C.2    Knowles, J.3
  • 20
    • 77954053914 scopus 로고    scopus 로고
    • Multi-scoring functions sampling in protein loop structure prediction
    • submitted to
    • Y. Li, I. Rata, E. Jakobsson, "Multi-Scoring Functions Sampling in Protein Loop Structure Prediction," submitted to Applied Mathematics and Computation, 2009.
    • (2009) Applied Mathematics and Computation
    • Li, Y.1    Rata, I.2    Jakobsson, E.3
  • 21
    • 67649535959 scopus 로고    scopus 로고
    • Improving consensus contact prediction via server correlation reduction
    • X. Gao, D. Bu, J. Xu, M. Li, "Improving Consensus Contact Prediction via Server Correlation Reduction," BMC Structural Biology, 9:28-42, 2009.
    • (2009) BMC Structural Biology , vol.9 , pp. 28-42
    • Gao, X.1    Bu, D.2    Xu, J.3    Li, M.4
  • 22
    • 34347327023 scopus 로고    scopus 로고
    • Pareto front analysis of flight time and energy use in long-distance bird migration
    • J. A. Vrugt, J. van Belle, W. Bouten, "Pareto front analysis of flight time and energy use in long-distance bird migration," Journal of Avian Biology, 38(4): 432:443, 2007.
    • (2007) Journal of Avian Biology , vol.38 , Issue.4 , pp. 432-443
    • Vrugt, J.A.1    Van Belle, J.2    Bouten, W.3
  • 23
    • 33847064673 scopus 로고    scopus 로고
    • Calibration of the NEMURO nutrient-phytoplankton-zooplankton food web model to a coastal ecosystem: Evaluation of an automated calibration approach
    • K. A. Rose, B. A. Megrey, F. E. Werner, D. M. Ware, "Calibration of the NEMURO nutrient-phytoplankton-zooplankton food web model to a coastal ecosystem: Evaluation of an automated calibration approach," Ecological Modelling, 202: 38-51, 2007.
    • (2007) Ecological Modelling , vol.202 , pp. 38-51
    • Rose, K.A.1    Megrey, B.A.2    Werner, F.E.3    Ware, D.M.4
  • 25
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • A. A. Canutescu, R. L. Dunbrack, "Cyclic Coordinate Descent: A robotics algorithm for protein loop closure," Protein Science, 12:963-972, 2003.
    • (2003) Protein Science , vol.12 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack, R.L.2
  • 27
    • 34548447184 scopus 로고    scopus 로고
    • Loopholes and missing links in protein modeling
    • K. R. Rossi, C. A. Weigelt, A. Nayeem, S. R. Krystek, "Loopholes and missing links in protein modeling," Protein Sci., 16(9):199- 2012, 2007.
    • (2007) Protein Sci. , vol.16 , Issue.9 , pp. 199-2012
    • Rossi, K.R.1    Weigelt, C.A.2    Nayeem, A.3    Krystek, S.R.4
  • 28
  • 29
    • 34547309668 scopus 로고    scopus 로고
    • Version 2.3. nVidia, Available at
    • nVidia, 2010, CUDA Programming Guide Version 2.3. nVidia, Available at: http://www.nvidia.com/object/cuda-get.html.
    • (2010) CUDA Programming Guide


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.