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Volumn , Issue , 2004, Pages 278-289

High-throughput 3D structural homology detection via NMR resonance assignment

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; AMINO ACIDS; DATABASE SYSTEMS; GRAPH THEORY; MATHEMATICAL MODELS; NUCLEAR MAGNETIC RESONANCE; PROTEINS; THREE DIMENSIONAL; THROUGHPUT;

EID: 14044266326     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/csb.2004.1332441     Document Type: Conference Paper
Times cited : (23)

References (45)
  • 1
    • 0034004003 scopus 로고    scopus 로고
    • A new approach for applying residual dipolar couplings as restraints in structure elucidation
    • MEILER, J. AND BLOMBERG, N. AND NILGES, M. AND GRIESINGER, C. A new approach for applying residual dipolar couplings as restraints in structure elucidation. Journal of Biomolecular NMR 16 (2000), 245-252.
    • (2000) Journal of Biomolecular NMR , vol.16 , pp. 245-252
    • Meiler, J.1    Blomberg, N.2    Nilges, M.3    Griesinger, C.4
  • 2
    • 0037433036 scopus 로고    scopus 로고
    • PDP: Protein domain parser
    • ALEXANDROV, N., AND SHINDYALOV, I. PDP: protein domain parser. Bioinformatics 19, 3 (2003), 429-430.
    • (2003) Bioinformatics , vol.19 , Issue.3 , pp. 429-430
    • Alexandrov, N.1    Shindyalov, I.2
  • 3
    • 0032841148 scopus 로고    scopus 로고
    • Recognition of protein folds via dipolar couplings
    • ANNILA, A. AND AITIO, H. AND THULIN, E. AND DRAKENBERG. T. Recognition of protein folds via dipolar couplings. J. Biom. NMR 14 (1999), 223-230.
    • (1999) J. Biom. NMR , vol.14 , pp. 223-230
    • Annila, A.1    Aitio, H.2    Thulin, E.3    Drakenberg, T.4
  • 4
    • 0033677333 scopus 로고    scopus 로고
    • The NOESY Jigsaw: Automated protein secondary structure and mainchain assignment from sparse, unassigned NMR data
    • BAILEY-KELLOGG, C. AND WIDGE, A. AND KELLEY III, J.J. AND BERARDI, M.J. AND BUSHWELLER, J.H. AND DONALD, B.R. The NOESY Jigsaw: automated protein secondary structure and mainchain assignment from sparse, unassigned NMR data. J Comput Biol 7, 3-4 (2000), 537-58.
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 537-558
    • Bailey-Kellogg, C.1    Widge, A.2    Kelley III, J.J.3    Berardi, M.O.4    Bushweller, J.H.5    Donald, B.R.6
  • 6
    • 0023305986 scopus 로고
    • Knowledgebased prediction of protein structures and the design of novel molecules
    • BLUNDELL, T.L. AND SIBANDA, B.L. AND STERNBERG, M.J. AND THORNTON, J.M. KnowledgeBased Prediction of Protein Structures and the Design of Novel Molecules. Nature 326 (1987), 347-352.
    • (1987) Nature , vol.326 , pp. 347-352
    • Blundell, T.L.1    Sibanda, B.L.2    Sternberg, M.J.3    Thornton, J.M.4
  • 8
    • 0032528033 scopus 로고    scopus 로고
    • Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
    • CORNILESCU, G. AND MARQUARDT, J. L. AND OTTIGER, M. AND BAX, A. Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase. J.Am.Chem.Soc. 120 (1998), 6836-6837.
    • (1998) J.Am.Chem.Soc. , vol.120 , pp. 6836-6837
    • Cornilescu, G.1    Marquardt, J.L.2    Ottiger, M.3    Bax, A.4
  • 10
    • 0033609905 scopus 로고    scopus 로고
    • Solution structure of gaip (galpha interacting protein): A regulator of G protein signaling
    • DE ALBA, E. AND DE VRIES, L. AND FARQUHAR, M. G. AND TJANDRA, N. Solution Structure of Gaip (Galpha Interacting Protein): A Regulator of G Protein Signaling. J.MolBiol. 291 (1999), 927.
    • (1999) J.MolBiol. , vol.291 , pp. 927
    • De Alba, E.1    De Vries, L.2    Farquhar, M.G.3    Tjandra, N.4
  • 12
    • 2442475806 scopus 로고    scopus 로고
    • Rapid protein structure detection and assignment using residual dipolar couplings
    • Carnegie Mellon University, Computer Science Department, School of Computer Science
    • ERDMANN, M.A. AND RULE, G. S. Rapid Protein Structure Detection and Assignment using Residual Dipolar Couplings. Tech. Rep. CMU-CS-02-195, Carnegie Mellon University, Computer Science Department, School of Computer Science, 2002.
    • (2002) Tech. Rep. , vol.CMU-CS-02-195
    • Erdmann, M.A.1    Rule, G.S.2
  • 13
    • 14744303317 scopus 로고
    • New programs for protein tertiary structure prediction
    • FETROW, J.S. AND BRYANT, S.H. New Programs for Protein Tertiary Structure Prediction. Bio/Technology 11 (1993), 479-484.
    • (1993) Bio/Technology , vol.11 , pp. 479-484
    • Fetrow, J.S.1    Bryant, S.H.2
  • 14
    • 0026320025 scopus 로고
    • Comparative modeling of homologous proteins
    • GREER, J. Comparative Modeling of Homologous Proteins. Meth. Enzymol. 202 (1991), 239-252.
    • (1991) Meth. Enzymol. , vol.202 , pp. 239-252
    • Greer, J.1
  • 16
    • 0025978283 scopus 로고
    • Database algorithm for generating protein backbone and side-chain coordinates from a C alpha trace application to model building and detection of co-ordinate errors
    • HOLM, L. AND SANDER, C. Database algorithm for generating protein backbone and side-chain coordinates from a C alpha trace application to model building and detection of co-ordinate errors. J. Mol. Biol. 218, 1 (1991), 183-194.
    • (1991) J. Mol. Biol. , vol.218 , Issue.1 , pp. 183-194
    • Holm, L.1    Sander, C.2
  • 17
    • 0036962374 scopus 로고    scopus 로고
    • Assignment strategy for proteins of known structure
    • Hus, J.C. AND PROPMERS, J. AND BRÜSCHWEILER, R. Assignment strategy for proteins of known structure. J. Mag. Res 157 (2002), 119-125.
    • (2002) J. Mag. Res , vol.157 , pp. 119-125
    • Hus, J.C.1    Propmers, J.2    Brüschweiler, R.3
  • 19
    • 0002719797 scopus 로고
    • Hungarian method for the assignment problem
    • KUHN, H.W. Hungarian method for the assignment problem. Nav. Res. Logist. Quarterly 2 (1955), 83-97.
    • (1955) Nav. Res. Logist. Quarterly , vol.2 , pp. 83-97
    • Kuhn, H.W.1
  • 20
    • 0033577269 scopus 로고    scopus 로고
    • Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration
    • KUSZEWSKI, J. AND GRONENBORN, A. M. AND CLORE, G. M. Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration. J. Am. Chem. Soc. 121 (1999), 2337-2338.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 2337-2338
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 21
    • 84960424236 scopus 로고    scopus 로고
    • 3DStructural homology detection via unassigned residual dipolar couplings
    • Stanford University, Palo Alto, CA (August 11-14)
    • LANGMEAD, C. J., AND DONALD, B. R. 3DStructural Homology Detection via Unassigned Residual Dipolar Couplings. Proc. IEEE Computer Society Bioinformatics Conference (CSB), Stanford University, Palo Alto, CA (August 11-14) (2003), 209-217.
    • (2003) Proc. IEEE Computer Society Bioinformatics Conference (CSB) , pp. 209-217
    • Langmead, C.J.1    Donald, B.R.2
  • 22
    • 1842555458 scopus 로고    scopus 로고
    • An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments
    • LANGMEAD, C. J., AND DONALD, B. R. An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. J. Biomol. NMR. 29, 2 (2004), 111-138.
    • (2004) J. Biomol. NMR , vol.29 , Issue.2 , pp. 111-138
    • Langmead, C.J.1    Donald, B.R.2
  • 23
    • 3142616097 scopus 로고    scopus 로고
    • An improved nuclear vector replacement algorithm for nuclear magnetic resonance assignment
    • Dartmouth Dept. of Computer Science
    • LANGMEAD, C. J., AND DONALD, B. R. An improved nuclear vector replacement algorithm for nuclear magnetic resonance assignment. Tech. Rep. TR2004-494, Dartmouth Dept. of Computer Science, 2004.
    • (2004) Tech. Rep. , vol.TR2004-494
    • Langmead, C.J.1    Donald, B.R.2
  • 24
    • 14044266505 scopus 로고    scopus 로고
    • A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments
    • In press
    • LANGMEAD, C. J., YAN, A. K., WANG, L., LILIEN, R. H., AND DONALD, B. R. A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. J. Comp. Bio. (2003). In press.
    • (2003) J. Comp. Bio.
    • Langmead, C.J.1    Yan, A.K.2    Wang, L.3    Lilien, R.H.4    Donald, B.R.5
  • 26
    • 0029912991 scopus 로고    scopus 로고
    • Global optimum protein threading with gapped alignment and empirical pair score functions
    • LATHROP, R.H. AND SMITH, T.F. Global Optimum Protein Threading with Gapped Alignment and Empirical Pair Score Functions. J. Mol. Biol. 255 (1996), 641-665.
    • (1996) J. Mol. Biol. , vol.255 , pp. 641-665
    • Lathrop, R.H.1    Smith, T.F.2
  • 27
    • 0033145058 scopus 로고    scopus 로고
    • Order matrix analysis of residual dipolar couplings using singular value decomposition
    • LOSONCZI, J.A. AND ANDREC, M. AND FISCHER, W.F. AND PRESTEGARD J.H. Order matrix analysis of residual dipolar couplings using singular value decomposition. J Magn Reson 138, 2 (1999), 334-42.
    • (1999) J Magn Reson , vol.138 , Issue.2 , pp. 334-342
    • Losonczi, J.A.1    Andrec, M.2    Fischer, W.F.3    Prestegard, J.H.4
  • 28
    • 0346103679 scopus 로고    scopus 로고
    • Rapid protein fold determination using unassigned NMR data
    • MEILER, J. AND BAKER, D. Rapid protein fold determination using unassigned NMR data. Proc. Natl. Acad. Sci. 100, 26 (2003), 15404-15409.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , Issue.26 , pp. 15404-15409
    • Meiler, J.1    Baker, D.2
  • 29
    • 3142582166 scopus 로고    scopus 로고
    • The National Institute of General Medical Sciences
    • NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES. The Protein Structure Initiative. The National Institute of General Medical Sciences, 2002. URL: http://www.nigms.nih.gov/psi/.
    • (2002) The Protein Structure Initiative.
  • 30
    • 0038407231 scopus 로고    scopus 로고
    • Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts
    • NEAL, S AND NIP, A. M. AND ZHANG, H. AND WlSHART, D. S. Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J. Biomol. NMR 26 (2003), 215-240.
    • (2003) J. Biomol. NMR , vol.26 , pp. 215-240
    • Neal, S.1    Nip, A.M.2    Zhang, H.3    Wlshart, D.S.4
  • 31
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structures and energies of molecules
    • PEARLMAN, D.A. AND CASE, D.A. AND CALDWELL, J.W. AND ROSS, W.S. AND CHEATHAM, T.E. AND DEBOUT, S. AND FERGUSON, D. AND SEIBEL, G. AND KOLLMAN, P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structures and energies of molecules. Comp. Phy. Comm. 91 (1995), 1-41.
    • (1995) Comp. Phy. Comm. , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    Debout, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 32
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • SALI, A. AND BLUNDELL, T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993), 779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 33
    • 0025350388 scopus 로고
    • From comparisons of protein sequences and structures to protein modelling and design
    • SALI, A. AND OVERINGTON, J.P. AND JOHNSON, M.S. AND BLUNDELL, T.L. From Comparisons of Protein Sequences and Structures to Protein Modelling and Design. Trends Biochem. Sci. 15 (1990), 235-240.
    • (1990) Trends Biochem. Sci. , vol.15 , pp. 235-240
    • Sali, A.1    Overington, J.P.2    Johnson, M.S.3    Blundell, T.L.4
  • 34
    • 84967789667 scopus 로고
    • Recent Results in the field of liquid crystals
    • SAUPE, A. Recent Results in the field of liquid crystals. Angew. Chem. 7 (1968), 97-112.
    • (1968) Angew. Chem. , vol.7 , pp. 97-112
    • Saupe, A.1
  • 36
    • 0026223896 scopus 로고
    • A relational database for sequence-specific protein NMR data
    • SEAVEY, B.R. AND FARR, E.A. AND WESTLER, W.M. AND MARKLEY, J.L. A Relational Database for Sequence-Specific Protein NMR Data. J. Biom. NMR 1 (1991), 217-236.
    • (1991) J. Biom. NMR , vol.1 , pp. 217-236
    • Seavey, B.R.1    Farr, E.A.2    Westler, W.M.3    Markley, J.L.4
  • 37
    • 0030722243 scopus 로고    scopus 로고
    • Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium
    • TJANDRA, N. AND BAX, A. Direct Measurement of Distances and Angles in Biomolecules by NMR in a Dilute Liquid Crystalline Medium. Science 278 (1997), 1111-1114.
    • (1997) Science , vol.278 , pp. 1111-1114
    • Tjandra, N.1    Bax, A.2
  • 38
    • 0029050883 scopus 로고
    • Nuclear magnetic dipole interactions in field-oriented proteins:information for structure determination in solution
    • TOLMAN, J. R., FLANAGAN, J. M., KENNEDY, M. A., AND PRESTEGARD, J. H. Nuclear magnetic dipole interactions in field-oriented proteins:information for structure determination in solution. Proc. Natl. Acad. Sci. USA 92 (1995), 9279-9283.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 9279-9283
    • Tolman, J.R.1    Flanagan, J.M.2    Kennedy, M.A.3    Prestegard, J.H.4
  • 39
    • 0042889106 scopus 로고    scopus 로고
    • Rapid classification of a protein fold family using a statistical analysis of dipolar couplings
    • VALAFAR, H. AND PRESTEGARD, J.H. Rapid classification of a protein fold family using a statistical analysis of dipolar couplings. Bioinformatics 19, 12 (2003), 1549-1555.
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1549-1555
    • Valafar, H.1    Prestegard, J.H.2
  • 40
    • 14044253051 scopus 로고    scopus 로고
    • Kluwer Academic Publishers, Van Godewijckstraat 30, P.O. Box 17, 3300 AA Dordrecht, The Netherlands
    • WÜTHRICH, K., Ed. The Journal of Biomolecular NMR. Kluwer Academic Publishers, Van Godewijckstraat 30, P.O. Box 17, 3300 AA Dordrecht, The Netherlands, 1997-2003.
    • The Journal of Biomolecular NMR , pp. 1997-2003
    • Wüthrich, K.1
  • 41
    • 0035544152 scopus 로고    scopus 로고
    • Automated prediction of 15N, 13C'alpha', 13C'beta' and 13C' chemical shifts in proteins using a density functional database
    • Xu, X.P AND CASE, D.A. Automated prediction of 15N, 13C'alpha', 13C'beta' and 13C' chemical shifts in proteins using a density functional database. J. Biomol. NMR 21 (2001), 321-333.
    • (2001) J. Biomol. NMR , vol.21 , pp. 321-333
    • Xu, X.P.1    Case, D.A.2
  • 42
    • 0033689127 scopus 로고    scopus 로고
    • Protein structure determination using protein threading and sparse NMR data
    • XU, Y. AND XU, D. AND CRAWFORD, O. H. AND EINSTEIN, J. R. AND SERPERSU, E. Protein Structure Determination Using Protein Threading and Sparse NMR Data. In Proc. RECOMB (2000), pp. 299-307.
    • (2000) Proc. RECOMB , pp. 299-307
    • Xu, Y.1    Xu, D.2    Crawford, O.H.3    Einstein, J.R.4    Serpersu, E.5
  • 44
    • 0034685436 scopus 로고    scopus 로고
    • Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR
    • ZWECKSTETTER, M., AND BAX, M. Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR. J. Am. Chem. Soc. 122 (2000), 3791-3792.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 3791-3792
    • Zweckstetter, M.1    Bax, M.2
  • 45
    • 0043027088 scopus 로고    scopus 로고
    • Determination of molecular alignment tensors without backbone resonance assignment: Aid to rapid analysis of protein-protein interactions
    • ZWECKSTETTER, M. Determination of molecular alignment tensors without backbone resonance assignment: Aid to rapid analysis of protein-protein interactions. J. Biomol. NMR 27, 1 (2003), 41-56.
    • (2003) J. Biomol. NMR , vol.27 , Issue.1 , pp. 41-56
    • Zweckstetter, M.1


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