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Volumn 56, Issue 4, 2013, Pages 337-351

PDBStat: A universal restraint converter and restraint analysis software package for protein NMR

Author keywords

BioMagResDatabase; CNS; CS Rosetta; CYANA; Protein NMR structure validation; XPLOR

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; LEARNING CURVE; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; VALIDATION PROCESS;

EID: 84883463996     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-013-9753-7     Document Type: Article
Times cited : (59)

References (53)
  • 1
    • 63549111769 scopus 로고    scopus 로고
    • Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy
    • 10.1371/journal.pcbi.1000307
    • Bahrami A, Assadi AH, Markley JL, Eghbalnia HR (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol 5:e1000307
    • (2009) PLoS Comput Biol , vol.5 , pp. 1000307
    • Bahrami, A.1    Assadi, A.H.2    Markley, J.L.3    Eghbalnia, H.R.4
  • 2
    • 4344648451 scopus 로고    scopus 로고
    • Automated analysis of protein NMR assignments and structures
    • 10.1021/cr030408p
    • Baran MC, Huang YJ, Moseley HN, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541-3556
    • (2004) Chem Rev , vol.104 , pp. 3541-3556
    • Baran, M.C.1    Huang, Y.J.2    Moseley, H.N.3    Montelione, G.T.4
  • 3
    • 33644847501 scopus 로고    scopus 로고
    • SPINS: A laboratory information management system for organizing and archiving intermediate and final results from NMR protein structure determinations
    • 10.1002/prot.20840
    • Baran MC, Moseley HN, Aramini JM, Bayro MJ, Monleon D, Locke JY, Montelione GT (2006) SPINS: a laboratory information management system for organizing and archiving intermediate and final results from NMR protein structure determinations. Proteins 62:843-851
    • (2006) Proteins , vol.62 , pp. 843-851
    • Baran, M.C.1    Moseley, H.N.2    Aramini, J.M.3    Bayro, M.J.4    Monleon, D.5    Locke, J.Y.6    Montelione, G.T.7
  • 4
    • 0030000521 scopus 로고    scopus 로고
    • Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints
    • 10.1002/pro.5560050404
    • Bassolino-Klimas D, Tejero R, Krystek SR, Metzler WJ, Montelione GT, Bruccoleri RE (1996) Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints. Protein Sci 5:593-603
    • (1996) Protein Sci , vol.5 , pp. 593-603
    • Bassolino-Klimas, D.1    Tejero, R.2    Krystek, S.R.3    Metzler, W.J.4    Montelione, G.T.5    Bruccoleri, R.E.6
  • 5
    • 33847079676 scopus 로고    scopus 로고
    • Evaluating protein structures determined by structural genomics consortia
    • 10.1002/prot.21165
    • Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778-795
    • (2007) Proteins , vol.66 , pp. 778-795
    • Bhattacharya, A.1    Tejero, R.2    Montelione, G.T.3
  • 6
    • 37349062680 scopus 로고    scopus 로고
    • Assessing model accuracy using the homology modeling automatically (HOMA) software
    • 10.1002/prot.21466
    • Bhattacharya A, Wunderlich Z, Monleon D, Tejero R, Montelione GT (2008) Assessing model accuracy using the homology modeling automatically (HOMA) software. Proteins 70:105-118
    • (2008) Proteins , vol.70 , pp. 105-118
    • Bhattacharya, A.1    Wunderlich, Z.2    Monleon, D.3    Tejero, R.4    Montelione, G.T.5
  • 7
    • 0022336792 scopus 로고
    • Calculation of protein conformations by proton-proton distance constraints: A new efficient algorithm
    • 10.1016/0022-2836(85)90134-2
    • Braun W, Go N (1985) Calculation of protein conformations by proton-proton distance constraints: a new efficient algorithm. J Mol Biol 186:611-626
    • (1985) J Mol Biol , vol.186 , pp. 611-626
    • Braun, W.1    Go, N.2
  • 9
    • 0032528033 scopus 로고    scopus 로고
    • Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
    • 10.1021/ja9812610
    • Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836-6837
    • (1998) J Am Chem Soc , vol.120 , pp. 6836-6837
    • Cornilescu, G.1    Marquardt, J.L.2    Ottiger, M.3    Bax, A.4
  • 10
    • 0029400480 scopus 로고
    • NMRPipe: A multidimensional spectral processing system based on UNIX pipes
    • 10.1007/BF00197809
    • Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293
    • (1995) J Biomol NMR , vol.6 , pp. 277-293
    • Delaglio, F.1    Grzesiek, S.2    Vuister, G.W.3    Zhu, G.4    Pfeifer, J.5    Bax, A.6
  • 11
    • 0033027208 scopus 로고    scopus 로고
    • Completeness of NOEs in protein structure: A statistical analysis of NMR data
    • 10.1023/A:1008335423527
    • Doreleijers JF, Raves ML, Rullmann T, Kaptein R (1999) Completeness of NOEs in protein structure: a statistical analysis of NMR data. J Biomol NMR 14:123-132
    • (1999) J Biomol NMR , vol.14 , pp. 123-132
    • Doreleijers, J.F.1    Raves, M.L.2    Rullmann, T.3    Kaptein, R.4
  • 12
    • 0037986814 scopus 로고    scopus 로고
    • BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank
    • 10.1023/A:1023514106644
    • Doreleijers JF, Mading S, Maziuk D, Sojourner K, Yin L, Zhu J, Markley JL, Ulrich EL (2003) BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J Biomol NMR 26:139-146
    • (2003) J Biomol NMR , vol.26 , pp. 139-146
    • Doreleijers, J.F.1    Mading, S.2    Maziuk, D.3    Sojourner, K.4    Yin, L.5    Zhu, J.6    Markley, J.L.7    Ulrich, E.L.8
  • 15
    • 0026089657 scopus 로고
    • Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA
    • 10.1016/0022-2836(91)90754-T
    • Güntert P, Braun W, Wüthrich K (1991) Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J Mol Biol 217:517-530
    • (1991) J Mol Biol , vol.217 , pp. 517-530
    • Güntert, P.1    Braun, W.2    Wüthrich, K.3
  • 16
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • 10.1006/jmbi.1997.1284
    • Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283-298
    • (1997) J Mol Biol , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 17
    • 80051673221 scopus 로고    scopus 로고
    • SHIFTX2: Significantly improved protein chemical shift prediction
    • 10.1007/s10858-011-9478-4
    • Han B, Liu Y, Ginzinger SW, Wishart DS (2011) SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR 50:43-57
    • (2011) J Biomol NMR , vol.50 , pp. 43-57
    • Han, B.1    Liu, Y.2    Ginzinger, S.W.3    Wishart, D.S.4
  • 18
    • 0022429234 scopus 로고
    • An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution
    • 10.1016/0022-2836(85)90346-8
    • Havel TF, Wüthrich K (1985) An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J Mol Biol 182:281-294
    • (1985) J Mol Biol , vol.182 , pp. 281-294
    • Havel, T.F.1    Wüthrich, K.2
  • 19
    • 84874810944 scopus 로고    scopus 로고
    • Vivaldi: Visualizaton and validation of biomacromolecular NMR structures from the PDB
    • Hendrickx PM, Gutmanas A, Kleywegt GJ (2013) Vivaldi: visualizaton and validation of biomacromolecular NMR structures from the PDB. Proteins 81:583-591
    • (2013) Proteins , vol.81 , pp. 583-591
    • Hendrickx, P.M.1    Gutmanas, A.2    Kleywegt, G.J.3
  • 20
    • 0036308102 scopus 로고    scopus 로고
    • Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
    • 10.1016/S0022-2836(02)00241-3
    • Herrmann T, Güntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209-227
    • (2002) J Mol Biol , vol.319 , pp. 209-227
    • Herrmann, T.1    Güntert, P.2    Wüthrich, K.3
  • 22
    • 13644252170 scopus 로고    scopus 로고
    • Protein NMR recall, precision and F-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics
    • 10.1021/ja047109h
    • Huang YJ, Powers R, Montelione GT (2005b) Protein NMR recall, precision and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665-1674
    • (2005) J Am Chem Soc , vol.127 , pp. 1665-1674
    • Huang, Y.J.1    Powers, R.2    Montelione, G.T.3
  • 23
    • 31944451135 scopus 로고    scopus 로고
    • A topology-constrained distance network algorithm for protein structure determination from NOESY data
    • 10.1002/prot.20820
    • Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins. 62:587-603
    • (2006) Proteins. , vol.62 , pp. 587-603
    • Huang, Y.J.1    Tejero, R.2    Powers, R.3    Montelione, G.T.4
  • 25
    • 0027092679 scopus 로고
    • The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures
    • 10.1002/pro.5560010606
    • Hyberts SG, Goldberg MS, Havel TF, Wagner G (1992) The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Sci 1:736-751
    • (1992) Protein Sci , vol.1 , pp. 736-751
    • Hyberts, S.G.1    Goldberg, M.S.2    Havel, T.F.3    Wagner, G.4
  • 26
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • 1976AcCrA.32.922K 10.1107/S0567739476001873
    • Kabsch W (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 32:922-923
    • (1976) Acta Crystallogr A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 27
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch W (1978) A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 34:827-828
    • (1978) Acta Crystallogr A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 28
    • 79955968115 scopus 로고    scopus 로고
    • Objective identification of residue ranges for the superposition of protein structures
    • 10.1186/1471-2105-12-170
    • Kirchner DK, Güntert P (2011) Objective identification of residue ranges for the superposition of protein structures. BMC Bioinformatics 12:170
    • (2011) BMC Bioinformatics , vol.12 , pp. 170
    • Kirchner, D.K.1    Güntert, P.2
  • 31
    • 0033145058 scopus 로고    scopus 로고
    • Order matrix analysis of residual dipolar couplings using singular value decomposition
    • 1999JMagR.138.334L 10.1006/jmre.1999.1754
    • Losonczi JA, Andrec M, Fischer MW, Prestegard JH (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, M.W.3    Prestegard, J.H.4
  • 32
    • 79958127392 scopus 로고    scopus 로고
    • Improved technologies now routinely provide protein NMR structures useful for molecular replacement
    • 10.1016/j.str.2011.04.005
    • Mao B, Guan R, Montelione GT (2011) Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Structure 19:757-766
    • (2011) Structure , vol.19 , pp. 757-766
    • Mao, B.1    Guan, R.2    Montelione, G.T.3
  • 34
    • 0032857781 scopus 로고    scopus 로고
    • Automated analysis of NMR assignments and structures for proteins
    • 10.1016/S0959-440X(99)00019-6
    • Moseley HN, Montelione GT (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
  • 35
    • 0034923123 scopus 로고    scopus 로고
    • Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data
    • 10.1016/S0076-6879(01)39311-4
    • Moseley HN, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol 339:91-108
    • (2001) Methods Enzymol , vol.339 , pp. 91-108
    • Moseley, H.N.1    Monleon, D.2    Montelione, G.T.3
  • 36
    • 1442306656 scopus 로고    scopus 로고
    • Assignment validation software suite for the evaluation and presentation of protein resonance assignment data
    • 10.1023/B:JNMR.0000015420.44364.06
    • Moseley HN, Sahota G, Montelione GT (2004) Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. J Biomol NMR 28:341-355
    • (2004) J Biomol NMR , vol.28 , pp. 341-355
    • Moseley, H.N.1    Sahota, G.2    Montelione, G.T.3
  • 37
    • 33645790319 scopus 로고    scopus 로고
    • Traditional biomolecular structure determination by NMR spectroscopy allows for major errors
    • 2006PLSCB.2.9N 10.1371/journal.pcbi.0020009
    • Nabuurs SB, Spronk CA, Vuister GW, Vriend G (2006) Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2:e9
    • (2006) PLoS Comput Biol , vol.2 , pp. 9
    • Nabuurs, S.B.1    Spronk, C.A.2    Vuister, G.W.3    Vriend, G.4
  • 38
    • 0028907436 scopus 로고
    • Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities
    • 10.1006/jmbi.1994.0053
    • Nilges M (1995) Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J Mol Biol 245:645-660
    • (1995) J Mol Biol , vol.245 , pp. 645-660
    • Nilges, M.1
  • 43
    • 0013293280 scopus 로고    scopus 로고
    • The Xplor-NIH NMR molecular structure determination package
    • 2003JMagR.160.65S 10.1016/S1090-7807(02)00014-9
    • Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65-73
    • (2003) J Magn Reson , vol.160 , pp. 65-73
    • Schwieters, C.D.1    Kuszewski, J.J.2    Tjandra, N.3    Clore, G.M.4
  • 44
    • 18844415920 scopus 로고    scopus 로고
    • Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
    • 10.1002/prot.20402
    • Snyder DA, Montelione GT (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins 59:673-686
    • (2005) Proteins , vol.59 , pp. 673-686
    • Snyder, D.A.1    Montelione, G.T.2
  • 45
    • 0002072348 scopus 로고    scopus 로고
    • Clustering in an object-oriented environment
    • Struyf A, Hubert M, Rousseeuw P (1996) Clustering in an object-oriented environment. J Stat Softw 1:1-30
    • (1997) J Stat Softw , vol.1 , pp. 1-30
    • Struyf, A.1    Hubert, M.2    Rousseeuw, P.3
  • 46
    • 0029920419 scopus 로고    scopus 로고
    • Simulated annealing with restrained molecular dynamics using CONGEN: Energy refinement of the NMR solution structures of epidermal and type-α transforming growth factors
    • 10.1002/pro.5560050403
    • Tejero R, Bassolino-Klimas D, Bruccoleri RE, Montelione GT (1996) Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-α transforming growth factors. Protein Sci 5:578-592
    • (1996) Protein Sci , vol.5 , pp. 578-592
    • Tejero, R.1    Bassolino-Klimas, D.2    Bruccoleri, R.E.3    Montelione, G.T.4
  • 47
    • 1642363964 scopus 로고    scopus 로고
    • REDCAT: A residual dipolar coupling analysis tool
    • 2004JMagR.167.228V 10.1016/j.jmr.2003.12.012
    • Valafar H, Prestegard JH (2004) REDCAT: a residual dipolar coupling analysis tool. J Magn Reson 167:228-241
    • (2004) J Magn Reson , vol.167 , pp. 228-241
    • Valafar, H.1    Prestegard, J.H.2
  • 50
  • 51
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • 10.1093/nar/gkg571
    • Zemla A (2003) LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 31:3370-3374
    • (2003) Nucleic Acids Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 53
    • 0034685436 scopus 로고    scopus 로고
    • Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR
    • 10.1021/ja0000908
    • Zweckstetter M, Bax A (2000) Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR. J Am Chem Soc 122:3791-3792
    • (2000) J Am Chem Soc , vol.122 , pp. 3791-3792
    • Zweckstetter, M.1    Bax, A.2


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