메뉴 건너뛰기




Volumn 21, Issue SUPPL. 1, 2005, Pages

High-throughput inference of protein-protein interfaces from unassigned NMR data

Author keywords

[No Author keywords available]

Indexed keywords

BARNASE; BARSTAR; UBIQUITIN;

EID: 29144506303     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1005     Document Type: Article
Times cited : (1)

References (43)
  • 2
    • 0033677333 scopus 로고    scopus 로고
    • The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data
    • Bailey-Kellogg,C., Widge,A., Kelley,J.J.III, Berardi,M.J., Bushweller,J.H. and Donald,B.R. (2000) The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. J. Comput. Biol., 7, 537-558.
    • (2000) J. Comput. Biol. , vol.7 , pp. 537-558
    • Bailey-Kellogg, C.1    Widge, A.2    Kelley III, J.J.3    Berardi, M.J.4    Bushweller, J.H.5    Donald, B.R.6
  • 4
    • 0028074974 scopus 로고
    • Protein-protein recognition: Crystal structural analysis of a barnase-barstar complex at 2.0-A resolution
    • Buckle,A.M., Schreiber,G. and Fersht,A.R. (1994) Protein-protein recognition: Crystal structural analysis of a barnase-barstar complex at 2.0-A resolution. Biochemistry, 33, 8878-8889.
    • (1994) Biochemistry , vol.33 , pp. 8878-8889
    • Buckle, A.M.1    Schreiber, G.2    Fersht, A.R.3
  • 6
    • 0026191608 scopus 로고
    • A singly exponential stratification scheme for real semi-algebraic varieties and its applications
    • Chazelle,B., Edelsbrunner,H., Guibas,L. and Sharir,M. (1991) A singly exponential stratification scheme for real semi-algebraic varieties and its applications. Theoretical Computer Science, 84, 77-105.
    • (1991) Theoretical Computer Science , vol.84 , pp. 77-105
    • Chazelle, B.1    Edelsbrunner, H.2    Guibas, L.3    Sharir, M.4
  • 7
    • 0034254909 scopus 로고    scopus 로고
    • Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization
    • Clore,G.M. (2000) Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization. Proc. Natl Acad. Sci. USA, 97, 9021-9025.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 9021-9025
    • Clore, G.M.1
  • 8
    • 0037433504 scopus 로고    scopus 로고
    • Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1H/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics
    • Clore,G.M. and Schwieters,C.D. (2003) Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1H/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics. J. Am. Chem. Soc., 125, 2902-2912.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 2902-2912
    • Clore, G.M.1    Schwieters, C.D.2
  • 9
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat,B.I. and Mayo,S.L. (1997) De novo protein design: Fully automated sequence selection. Science, 278, 82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 11
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez,C., Boelens,R. and Bonvin,A.M.J.J. (2003) HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 14
    • 2442475806 scopus 로고    scopus 로고
    • Rapid protein structure detection and assignment using residual dipolar copulings
    • Technical Report 195, Department of Computer Science, Carnegie-Mellon University, PA
    • Erdmann,M.A. and Rule,G.S. (2002) Rapid protein structure detection and assignment using residual dipolar copulings. Technical Report 195, Department of Computer Science, Carnegie-Mellon University, PA.
    • (2002)
    • Erdmann, M.A.1    Rule, G.S.2
  • 15
    • 0032939176 scopus 로고    scopus 로고
    • Solution structure of the 40 000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr
    • Garrett,D.S., Seok,Y.-J., Peterkofsky,A., Gronenborn,A.M. and Clore,G.M. (1999) Solution structure of the 40 000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr. Nat. Struct. Biol., 6, 166-173.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 166-173
    • Garrett, D.S.1    Seok, Y.-J.2    Peterkofsky, A.3    Gronenborn, A.M.4    Clore, G.M.5
  • 16
    • 0027690254 scopus 로고
    • Measurement of amide proton exchange rates and NOEs with water in 13C/15N-enriched calcineurin B
    • Grzesiek,S. and Bax,A. (1993) Measurement of amide proton exchange rates and NOEs with water in 13C/15N-enriched calcineurin B. J. Biomol. NMR, 3, 627-638.
    • (1993) J. Biomol. NMR , vol.3 , pp. 627-638
    • Grzesiek, S.1    Bax, A.2
  • 18
    • 0001798952 scopus 로고    scopus 로고
    • Arrangements
    • Goodman,J.E. and O'Rourke,J. (eds), CRC Press, New York, NY
    • Halperin,D. Arrangements. In Goodman,J.E. and O'Rourke,J. (eds), Handbook of Discrete and Computational Geometry. CRC Press, New York, NY, pp. 389-412.
    • Handbook of Discrete and Computational Geometry , pp. 389-412
    • Halperin, D.1
  • 19
  • 21
    • 84960424236 scopus 로고    scopus 로고
    • 3D structural homology detection via unassigned residual dipolar couplings
    • Stanford, CA
    • Langmead,C.J. and Donald,B.R. (2003) 3D structural homology detection via unassigned residual dipolar couplings. Proceedings of IEEE CSB 2003, Stanford, CA, pp. 209-217.
    • (2003) Proceedings of IEEE CSB 2003 , 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. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR, 29, 111-138.
    • (2004) J. Biomol. NMR , vol.29 , pp. 111-138
    • Langmead, C.J.1    Donald, B.R.2
  • 23
    • 3142588772 scopus 로고    scopus 로고
    • A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments
    • Langmead,C.J., Yan,A.K., Wang,L., Lilien,R.H. and Donald,B.R. (2004) A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. J. Comput. Biol., 11, 277-298.
    • (2004) J. Comput. Biol. , vol.11 , pp. 277-298
    • Langmead, C.J.1    Yan, A.K.2    Wang, L.3    Lilien, R.H.4    Donald, B.R.5
  • 24
    • 29144485663 scopus 로고    scopus 로고
    • Technical Report 492, Computer Science Department, Dartmouth College, NH
    • Lilien,R.H., Sridharan,M. and Donald,B.R. (2004) Technical Report 492, Computer Science Department, Dartmouth College, NH, http://www.cs.dartmouth.edu/reports/
    • (2004)
    • Lilien, R.H.1    Sridharan, M.2    Donald, B.R.3
  • 25
    • 0033145058 scopus 로고    scopus 로고
    • Order matrix analysis of residual dipolar couplings using singular value decomposition
    • Losonczi,J.A., Andrec,M., Fischer,W.F. and Prestegard J.H., (1999) Order matrix analysis of residual dipolar couplings using singular value decomposition. J. Magn. Reson., 138, 334-342.
    • (1999) J. Magn. Reson. , vol.138 , pp. 334-342
    • Losonczi, J.A.1    Andrec, M.2    Fischer, W.F.3    Prestegard, J.H.4
  • 26
    • 0037070536 scopus 로고    scopus 로고
    • Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations
    • McCoy,M.A. and Wyss,D.F. (2002) Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations. J. Am. Chem. Soc., 124, 2104-2105.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 2104-2105
    • McCoy, M.A.1    Wyss, D.F.2
  • 27
    • 29144522899 scopus 로고    scopus 로고
    • High-throughput inference of protein-protein interaction sites from unassinged NMR data by analyzing arrangements induced by quadratic forms on 3-manifolds
    • Computer Science Department, Dartmouth College, NH
    • Mettu,R.R., Lilien,R.H. and Donald,B.R. (2005) High-throughput inference of protein-protein interaction sites from unassinged NMR data by analyzing arrangements induced by quadratic forms on 3-manifolds. Computer Science Department, Dartmouth College, NH, http://www.cs.darkmouth.edu/reports/
    • (2005)
    • Mettu, R.R.1    Lilien, R.H.2    Donald, B.R.3
  • 29
    • 0032857781 scopus 로고    scopus 로고
    • Automated analysis of NMR assignments and structures for proteins
    • Moseley,H.N. and Montelione,G.T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol., 9, 635-642.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 635-642
    • Moseley, H.N.1    Montelione, G.T.2
  • 30
    • 29144518519 scopus 로고    scopus 로고
    • The Protein Structure Initiative
    • National Institute of General Medical Sciences, National Institutes of Health
    • National Institute of General Medical Sciences, National Institutes of Health. (2001) The Protein Structure Initiative, http://www.nigms.nih.gov/psi
    • (2001)
  • 31
    • 0033869869 scopus 로고    scopus 로고
    • Structure of the heterodimeric complex between CAD domains of CAD and ICAD
    • Otomo,T., Sakahira,H., Uegaki,K., Nagata,S. and Yamazaki,T. (2000) Structure of the heterodimeric complex between CAD domains of CAD and ICAD. Nat. Struct. Biol., 7, 658-662.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 658-662
    • Otomo, T.1    Sakahira, H.2    Uegaki, K.3    Nagata, S.4    Yamazaki, T.5
  • 32
    • 3242745225 scopus 로고    scopus 로고
    • Automated evaluation of chemical shift perturbation spectra: New approaches to quantitative analysis of receptor-ligand interaction NMR spectra
    • Peng,C., Unger,S.W., Filipp,F.V., Sattler,M. and Szalma,S. (2004) Automated evaluation of chemical shift perturbation spectra: New approaches to quantitative analysis of receptor-ligand interaction NMR spectra. J. Biomol. NMR, 29, 491-504.
    • (2004) J. Biomol. NMR , vol.29 , pp. 491-504
    • Peng, C.1    Unger, S.W.2    Filipp, F.V.3    Sattler, M.4    Szalma, S.5
  • 33
    • 0344875222 scopus 로고    scopus 로고
    • Fast mapping of protein-protein interfaces by NMR spectroscopy
    • Reese,M.L. and Dötsch,V. (2003) Fast mapping of protein-protein interfaces by NMR spectroscopy. J. Am. Chem. Soc., 125, 14250-14251.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14250-14251
    • Reese, M.L.1    Dötsch, V.2
  • 35
    • 84967789667 scopus 로고
    • Recent results in the field of liquid crystals
    • Saupe,A. (1968) Recent results in the field of liquid crystals. Angew. Chem., 7, 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., Farr,E.A., Westler,W.M. and Markley,J.L. (1991) A relational database for sequence-specific protein NMR data. J. Biomol. NMR, 1, 217-236.
    • (1991) J. Biomol. NMR , vol.1 , pp. 217-236
    • Seavey, B.R.1    Farr, E.A.2    Westler, W.M.3    Markley, J.L.4
  • 37
    • 0029836953 scopus 로고    scopus 로고
    • Discovering high-affinity ligands for proteins: SAR by NMR
    • Shuker,S.B., Hajduk,P.J., Meadows,R.P. and Fesik,S.W. (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science, 274, 1531-1534.
    • (1996) Science , vol.274 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 38
    • 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. (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science, 278, 1111-1114.
    • (1997) Science , vol.278 , pp. 1111-1114
    • Tjandra, N.1    Bax, A.2
  • 39
    • 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. (1995) Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. Proc. Natl Acad. Sci. USA, 92, 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
  • 40
    • 0042889106 scopus 로고    scopus 로고
    • Rapid classification of a protein fold family using a stati dipolar couplings
    • Valafar,H. and Prestegard,J.H. (2003) Rapid classification of a protein fold family using a stati dipolar couplings. Bioinformatics, 19(12), 1549-1555.
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1549-1555
    • Valafar, H.1    Prestegard, J.H.2
  • 41
    • 3042719896 scopus 로고    scopus 로고
    • Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure
    • Wang,L. and Donald,B.R. (2004) Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure. J. Biomol. NMR, 29, 223-242.
    • (2004) J. Biomol. NMR , vol.29 , pp. 223-242
    • Wang, L.1    Donald, B.R.2
  • 42
    • 0037039335 scopus 로고    scopus 로고
    • Mapping protein-protein interactions in solution by NMR spectroscopy
    • Zuiderweg,E.R.P. (2002) Mapping protein-protein interactions in solution by NMR spectroscopy. Biochemistry, 41, 1-7.
    • (2002) Biochemistry , vol.41 , pp. 1-7
    • Zuiderweg, E.R.P.1
  • 43
    • 0035955207 scopus 로고    scopus 로고
    • Single-step determination of protein substructures using dipolar couplings: Aid to structural genomics
    • Zweckstetter,M. and Bax,A. (2001) Single-step determination of protein substructures using dipolar couplings: Aid to structural genomics. J. Am. Chem. Soc., 123, 9490-9491.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 9490-9491
    • Zweckstetter, M.1    Bax, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.