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Volumn 9, Issue 1, 2011, Pages 15-41

Error tolerant nmr backbone resonance assignment and automated structure generation

Author keywords

backbone resonance assignment; NMR; protein structure determination

Indexed keywords

PROTEIN;

EID: 79851507501     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720011005276     Document Type: Article
Times cited : (24)

References (53)
  • 1
    • 0000714031 scopus 로고    scopus 로고
    • Automated sequence-specific NMR assignment of homologous proteins using the program GARANT
    • Bartels C, Billeter M, Güntert P. and Wüthrich K, Automated sequence-specific NMR assignment of homologous proteins using the program garant, J Biomol NMR 7: 207-213, 1996. (Pubitemid 126709559)
    • (1996) Journal of Biomolecular NMR , vol.7 , Issue.3 , pp. 207-213
    • Bartels, C.1    Billeter, M.2    Guntert, P.3    Wuthrich, K.4
  • 4
    • 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, Kelly J, Brushweller J, Donald BR, The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data, J Comput Biol 7:537-558, 2000.
    • (2000) J Comput Biol , vol.7 , pp. 537-558
    • Bailey-Kellogg, C.1    Widge, A.2    Kelly, J.3    Brushweller, J.4    Donald, B.R.5
  • 5
    • 0033757115 scopus 로고    scopus 로고
    • Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER
    • Güntert P, Salzmann M, Braun D, Wüthrich K, Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER, J Biomol NMR 18:129-137, 2000.
    • (2000) J Biomol NMR , vol.18 , pp. 129-137
    • Güntert, P.1    Salzmann, M.2    Braun, D.3    Wüthrich, K.4
  • 6
    • 0035965759 scopus 로고    scopus 로고
    • A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones
    • DOI 10.1021/ja011806h
    • Tian F, Valafar H, Prestegard JH, A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones, J Amer Chem Soc 123(47):11791-11796, 2001. (Pubitemid 33121799)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.47 , pp. 11791-11796
    • Tian, F.1    Valafar, H.2    Prestegard, J.H.3
  • 8
    • 0036962374 scopus 로고    scopus 로고
    • Assignment strategy for proteins with known structure
    • Hus JC, Prompers J, Brüschweiler R, Assignment strategy for proteins with known structure, J Magn Reson 157:119-123, 2002.
    • (2002) J Magn Reson , vol.157 , pp. 119-123
    • Hus, J.C.1    Prompers, J.2    Brüschweiler, R.3
  • 9
    • 2442475806 scopus 로고    scopus 로고
    • Rapid protein structure detection and assignment using residual dipolar couplings
    • School of computer science, Carnegie Mellon University, Pittsburgh, PA
    • Erdmann MA, Rule GS, Rapid protein structure detection and assignment using residual dipolar couplings, Technical Report CMU-CS-02-195, School of computer science, Carnegie Mellon University, Pittsburgh, PA, 2002.
    • (2002) Technical Report CMU-CS-02-195
    • Erdmann, M.A.1    Rule, G.S.2
  • 10
    • 0036462495 scopus 로고    scopus 로고
    • Semiautomatic sequence-specific assignment of proteins based on the tertiary structure-the program st2nmr
    • DOI 10.1002/jcc.10011
    • Pristovsek P, Rüterjans H, Jerala R, Semiautomatic sequence-specific assignment of proteins based on the tertiary structure - the program st2nmr, J Comput Chem 23:335-340, 2002. (Pubitemid 34137473)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.3 , pp. 335-340
    • Pristovek, P.1    Ruterjans, H.2    Jerala, R.3
  • 11
    • 0038663223 scopus 로고    scopus 로고
    • PACES: Protein sequential assignment by computer-assisted exhaustive search
    • DOI 10.1023/A:1023589029301
    • Coggins B, Zhou P, PACES: Protein sequential assignment by computer-assisted exhaustive search, J Biomol NMR 26:93-111, 2003. (Pubitemid 36609043)
    • (2003) Journal of Biomolecular NMR , vol.26 , Issue.2 , pp. 93-111
    • Coggins, B.E.1    Zhou, P.2
  • 12
    • 1542285879 scopus 로고    scopus 로고
    • α chemical shifts
    • DOI 10.1023/B:JNMR.0000019500.76436.31
    • Morris LC, Valafar H, Prestegard JH, Assignment of protein backbone resonances using connectivity, torsion angles and 13calpha chemical shifts, J Biomol NMR 29(1):1-9, May 2004. (Pubitemid 38324869)
    • (2004) Journal of Biomolecular NMR , vol.29 , Issue.1 , pp. 1-9
    • Morris, L.C.1    Valafar, H.2    Prestegard, J.H.3
  • 13
    • 4644234334 scopus 로고    scopus 로고
    • Mars - Robust automatic backbone assignment of proteins
    • DOI 10.1023/B:JNMR.0000042954.99056.ad
    • Jung Y, Zweckstetter M, Mars - robust automatic backbone assignment of proteins, J Biomol NMR 30:11-23, 2004. (Pubitemid 39295128)
    • (2004) Journal of Biomolecular NMR , vol.30 , Issue.1 , pp. 11-23
    • Jung, Y.-S.1    Zweckstetter, M.2
  • 14
    • 1842555458 scopus 로고    scopus 로고
    • An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments
    • DOI 10.1023/B:JNMR.0000019247.89110.e6
    • Langmead CJ, Donald BR, An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments, J Biomol NMR 29:111-138, 2004. (Pubitemid 38444475)
    • (2004) Journal of Biomolecular NMR , vol.29 , Issue.2 , pp. 111-138
    • Langmead, C.J.1    Donald, B.R.2
  • 15
    • 3142588772 scopus 로고    scopus 로고
    • A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments
    • DOI 10.1089/1066527041410436
    • Langmead CJ, Yan A, Lilien R, Wang L, Donald BR, A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignment, J Comput Biol 11:277-298, 2004. (Pubitemid 38901664)
    • (2004) Journal of Computational Biology , vol.11 , Issue.2-3 , pp. 277-298
    • Langmead, C.J.1    Yan, A.2    Lilien, R.3    Wang, L.4    Donald, B.R.5
  • 16
    • 15844385659 scopus 로고    scopus 로고
    • AutoLink: Automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic
    • DOI 10.1016/j.jmr.2005.01.017, PII S1090780705000108
    • Masse JE, Keller R, Autolink: Automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic, J Magn Reson 174:133-151, 2005. (Pubitemid 40423617)
    • (2005) Journal of Magnetic Resonance , vol.174 , Issue.1 , pp. 133-151
    • Masse, J.E.1    Keller, R.2
  • 17
    • 24344440618 scopus 로고    scopus 로고
    • Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO)
    • DOI 10.1007/s10858-005-7944-6
    • Eghbalnia HR, Bahrami A, Wang L, Assadi A, Markley JL, Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO), J Biomol NMR 32(3):219-233, 2005. (Pubitemid 41258802)
    • (2005) Journal of Biomolecular NMR , vol.32 , Issue.3 , pp. 219-233
    • Eghbalnia, H.R.1    Bahrami, A.2    Wang, L.3    Assadi, A.4    Markley, J.L.5
  • 19
    • 33645724050 scopus 로고    scopus 로고
    • Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data
    • Pristovsek P, Franzoni L, Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data, J Comput Chem 27:791-797, 2004.
    • (2004) J Comput Chem , vol.27 , pp. 791-797
    • Pristovsek, P.1    Franzoni, L.2
  • 20
    • 33645959198 scopus 로고    scopus 로고
    • RIBRA: An error-tolerant algorithm for the NMR backbone assignment problem
    • Wu K, Chang J, Chen J, Chang C, Wu W, Huang T, Sung T, Hsu W, RIBRA: An error-tolerant algorithm for the NMR backbone assignment problem, J Comput Biol 13(2):229-244, 2006.
    • (2006) J Comput Biol , vol.13 , Issue.2 , pp. 229-244
    • Wu, K.1    Chang, J.2    Chen, J.3    Chang, C.4    Wu, W.5    Huang, T.6    Sung, T.7    Hsu, W.8
  • 21
    • 34347373817 scopus 로고    scopus 로고
    • CISA: Combined NMR resonance connectivity information determination and sequential assignment
    • DOI 10.1109/TCBB.2007.1047
    • Wan X, Lin G, CISA: Combined NMR resonance connectivity information determination and sequential assignment, IEEE/ACM Trans Comput Biol Bioinformatics 4:336-348, 2007. (Pubitemid 47274712)
    • (2007) IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol.4 , Issue.3 , pp. 336-348
    • Wan, X.1    Lin, G.2
  • 22
    • 43649085607 scopus 로고    scopus 로고
    • Llińas M, Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach
    • Lemak A, Steren CA, Arrowsmith CH, Llińas M, Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach, J Biomol NMR 41:29-41, 2008.
    • (2008) J Biomol NMR , vol.41 , pp. 29-41
    • Lemak, A.1    Steren, C.A.2    Arrowsmith, C.H.3
  • 23
    • 46949106433 scopus 로고    scopus 로고
    • Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH
    • Volk J, Herrmann T, Wüthrich K, Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH, J Biomol NMR 41:127-138, 2008.
    • (2008) J Biomol NMR , vol.41 , pp. 127-138
    • Volk, J.1    Herrmann, T.2    Wüthrich, K.3
  • 25
    • 46249086182 scopus 로고    scopus 로고
    • Contact replacement for NMR resonance assignment
    • DOI 10.1093/bioinformatics/btn167
    • Xiong F, Pandurangan G, Bailey-Kellogg C, Contact replacement for NMR resonance assignment, Bioinformatics 24:i205-i213, 2008. (Pubitemid 351911675)
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Xiong, F.1    Pandurangan, G.2    Bailey-Kellogg, C.3
  • 26
    • 79951810315 scopus 로고
    • Automated amino acid sidechain NMR assignment of proteins using 13C and 15N-resolved 3D [1H,1 H]-NOESY
    • Fiorito F, Herrmann T, Damberger FF, Wüthrich K, Automated amino acid sidechain NMR assignment of proteins using 13C and 15N-resolved 3D [1H,1 H]-NOESY, J Algorithms 7:309-322, 1986.
    • (1986) J Algorithms , vol.7 , pp. 309-322
    • Fiorito, F.1    Herrmann, T.2    Damberger, F.F.3    Wüthrich, K.4
  • 27
    • 52049125539 scopus 로고    scopus 로고
    • Structure-based protein NMR assignments using native structural ensembles
    • Apaydin SM, Conitzer V, Donald BR, Structure-based protein NMR assignments using native structural ensembles, J Biomol NMR 40:263-276, 2008.
    • (2008) J Biomol NMR , vol.40 , pp. 263-276
    • Apaydin, S.M.1    Conitzer, V.2    Donald, B.R.3
  • 28
    • 60149087377 scopus 로고    scopus 로고
    • NOEnet - Use of NOE networks for NMR resonance assignment of proteins with known 3D structure
    • Stratmann D, Heijenoort C, Guittet E, NOEnet - use of NOE networks for NMR resonance assignment of proteins with known 3D structure, Bioinformatics 25(4): 474-481, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.4 , pp. 474-481
    • Stratmann, D.1    Heijenoort, C.2    Guittet, E.3
  • 29
    • 73949142822 scopus 로고    scopus 로고
    • NVR-BIP: Nuclear vector replacement using binary interger programming for NMR structure-based assignments
    • in press
    • Apaydin SM, Catay B, Patrick N, Donald B, NVR-BIP: Nuclear vector replacement using binary interger programming for NMR structure-based assignments, Computer J 2009. in press.
    • (2009) Computer J
    • Apaydin, S.M.1    Catay, B.2    Patrick, N.3    Donald, B.4
  • 30
    • 67650473269 scopus 로고    scopus 로고
    • Automated NMR assignment and protein structure determination using sparse dipolar coupling constraints
    • Donald B, Martin J, Automated NMR assignment and protein structure determination using sparse dipolar coupling constraints, Progress Nuclear Magn Reson Spectroscopy 55(2):101-127, 2009.
    • (2009) Progress Nuclear Magn Reson Spectroscopy , vol.55 , Issue.2 , pp. 101-127
    • Donald, B.1    Martin, J.2
  • 31
    • 0026223896 scopus 로고
    • A relational database for sequencespecific protein NMR data
    • Seavey BR, Farr EA, Westler WM, Markley J, A relational database for sequencespecific protein NMR data, J Biomol NMR 1:217-236, 1991.
    • (1991) J Biomol NMR , vol.1 , pp. 217-236
    • Seavey, B.R.1    Farr, E.A.2    Westler, W.M.3    Markley, J.4
  • 33
    • 33745364809 scopus 로고    scopus 로고
    • Automated resonance assignment of proteins: 6D APSY-NMR
    • DOI 10.1007/s10858-006-0030-x
    • Fiorito F, Hiller S,Wider G,Wüthrich K, Automated resonance assignment of protein: 6D APSY-NMR, J Biomol NMR 35:27-37, 2006. (Pubitemid 43941721)
    • (2006) Journal of Biomolecular NMR , vol.35 , Issue.1 , pp. 27-37
    • Fiorito, F.1    Hiller, S.2    Wider, G.3    Wuthrich, K.4
  • 35
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • DOI 10.1093/bioinformatics/btl158
    • Li W, Godzik A, CD-HIT: A fast program for clustering and comparing large sets of protein for nucleotide sequences, Bioinformatics 22:1658-1659, 2006. (Pubitemid 43985301)
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 36
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22(12):2577-2637, 1993.
    • (1993) Biopolymers , vol.22 , Issue.12 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 37
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin LJ, Bryson K, Jones DT, The PSIPRED protein structure prediction server, Bioinformatics 16(4):404-405, 2000. (Pubitemid 30417087)
    • (2000) Bioinformatics , vol.16 , Issue.4 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 40
    • 40849134012 scopus 로고    scopus 로고
    • The NMR structure of the Staphylococcus aureus response regulator VraR DNA binding domain reveals a dynamic relationship between it and its associated receiver domain
    • DOI 10.1021/bi701844q
    • Donaldson LW, The NMR structure of the Staphylococcus aureus response regulator VraR DNA binding domain reveals a dynamic relationship between it and its associated receiver domain, Biochemistry 47(11):3379-3388, 2008. (Pubitemid 351399226)
    • (2008) Biochemistry , vol.47 , Issue.11 , pp. 3379-3388
    • Donaldson, L.W.1
  • 41
    • 4544229498 scopus 로고    scopus 로고
    • Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings
    • DOI 10.1002/anie.200353588
    • Jung YS, Sharma M, Zweckstetter M, Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings, Angewandte Chemie (International ed. in English) 43(26):3479-3481, 2004. (Pubitemid 39257570)
    • (2004) Angewandte Chemie - International Edition , vol.43 , Issue.26 , pp. 3479-3481
    • Jung, Y.-S.1    Sharma, M.2    Zweckstetter, M.3
  • 42
    • 33749524593 scopus 로고    scopus 로고
    • Automated protein structure determination from NMR spectra
    • DOI 10.1021/ja061136l
    • Ĺopez-Ḿendez B, Güntert P, Automated protein structure determination from NMR spectra, J Am Chem Soc 128(40):13112-13122, 2006. (Pubitemid 44527681)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.40 , pp. 13112-13122
    • Lopez-Mendez, B.1    Guntert, P.2
  • 44
    • 58149468410 scopus 로고    scopus 로고
    • De novo protein structure generation from incomplete chemical shift assignments
    • Shen Y, Vernon R, Baker D, Bax A, De novo protein structure generation from incomplete chemical shift assignments, J Biomol NMR 43(2):63-78, 2009.
    • (2009) J Biomol NMR , vol.43 , Issue.2 , pp. 63-78
    • Shen, Y.1    Vernon, R.2    Baker, D.3    Bax, A.4
  • 45
    • 55549086519 scopus 로고    scopus 로고
    • Fragment-HMM: A new approach to protein structure prediction
    • Li SC, Bu D, Xu J, Li M, Fragment-HMM: A new approach to protein structure prediction, Protein Sci 17(11):1925-1934, 2008.
    • (2008) Protein Sci , vol.17 , Issue.11 , pp. 1925-1934
    • Li, S.C.1    Bu, D.2    Xu, J.3    Li, M.4
  • 46
    • 0242369082 scopus 로고    scopus 로고
    • RAPTOR: Optimal protein threading by linear programming
    • Xu J, Li M, Kim D, Xu Y, RAPTOR: Optimal protein threading by linear programming, J Bioinformatics Comput Biol 1:95-117, 2003.
    • (2003) J Bioinformatics Comput Biol , vol.1 , pp. 95-117
    • Xu, J.1    Li, M.2    Kim, D.3    Xu, Y.4
  • 48
    • 24944493938 scopus 로고    scopus 로고
    • Biochemistry: Toward high-resolution de novo structure prediction for small proteins
    • DOI 10.1126/science.1113801
    • Bradley P, Misura KMS, Baker D, Toward high-resolution de novo structure prediction for small proteins, Science 309:1868-1871, 2005. (Pubitemid 41325099)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 49
    • 75749131030 scopus 로고    scopus 로고
    • Can we determine a protein structure quickly?
    • Li M, Can we determine a protein structure quickly? J Computer Sci Technol 25(1):95-106, 2010.
    • (2010) J Computer Sci Technol , vol.25 , Issue.1 , pp. 95-106
    • Li, M.1
  • 53
    • 46249124995 scopus 로고    scopus 로고
    • Designing succinct structural alphabets
    • DOI 10.1093/bioinformatics/btn165
    • Li SC, Bu D, Gao X, Xu J, Li M, Designing succinct structural alphabets, Bioinformatics 24(13):i182-i189, 2008. (Pubitemid 351911672)
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Li, S.C.1    Bu, D.2    Gao, X.3    Xu, J.4    Li, M.5


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