Automated structure determination from NMR spectra

Altieri AS, Byrd RA (2004) Automation of NMR structure determination of proteins. Curr Opin Struct Biol 14:547–553. doi: 10.1016/j.sbi.2004.09.003

Andrec M, Levy RM (2002) Protein sequential resonance assignments by combinatorial enumeration using 13Cα chemical shifts and their (i, i − 1) sequential connectivities. J Biomol NMR 23:263–270. doi: 10.1023/A:1020236105735

Antz C, Neidig KP, Kalbitzer HR (1995) A general Bayesian method for an automated signal class recognition in 2D NMR spectra combined with a multivariate discriminant analysis. J Biomol NMR 5:287–296. doi: 10.1007/BF00211755

Atkinson RA, Saudek V (1997) Direct fitting of structure and chemical shift to NMR spectra. J Chem Soc Faraday Trans 93:3319–3323. doi: 10.1039/a702834b

Atkinson RA, Saudek V (2002) The direct determination of protein structure by NMR without assignment. FEBS Lett 510:1–4

Atreya HS, Szyperski T (2005) Rapid NMR data collection. Methods Enzymol 394:78–108. doi: 10.1016/S0076-6879(05)94004-4

Atreya HS, Sahu SC, Chary KVR, Govil G (2000) A tracked approach for automated NMR assignments in proteins (TATAPRO). J Biomol NMR 17:125–136. doi: 10.1023/A:1008315111278

Atreya HS, Chary KVR, Govil G (2002) Automated NMR assignments of proteins for high throughput structure determination: TATAPRO II. Curr Sci 83:1372–1376

Bailey-Kellogg C, Widge A, Kelley JJ, Berardi MJ, Bushweller JH, Donald BR (2000) The NOESY JIGSAW: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. J Comput Biol 7:537–558. doi: 10.1089/106652700750050934

Bailey-Kellogg C, Chainraj S, Pandurangan G (2005) A random graph approach to NMR sequential assignment. J Comput Biol 12:569–583. doi: 10.1089/cmb.2005.12.569

Baran MC, Huang YJ, Moseley HNB, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541–3555. doi: 10.1021/cr030408p

Bartels C, Xia TH, Billeter M, Güntert P, Wüthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1–10. doi: 10.1007/BF00417486

Bartels C, Billeter M, Güntert P, Wüthrich K (1996) Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR 7:207–213. doi: 10.1007/BF00202037

Bartels C, Güntert P, Billeter M, Wüthrich K (1997) GARANT: a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comput Chem 18:139–149. doi:10.1002/(SICI)1096-987X(19970115)18:1<139::AID-JCC13>3.0.CO;2-H

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H et al (2000) The protein data bank. Nucleic Acids Res 28:235–242. doi: 10.1093/nar/28.1.235

Bernstein R, Cieslar C, Ross A, Oschkinat H, Freund J, Holak TA (1993) Computer-assisted assignment of multidimensional NMR spectra of proteins—application to 3D NOESY-HMQC and TOCSY-HMQC Spectra. J Biomol NMR 3:245–251. doi: 10.1007/BF00178267

Bhavesh NS, Panchal SC, Hosur RV (2001) An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR. Biochemistry 40:14727–14735. doi: 10.1021/bi015683p

Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868–1871. doi: 10.1126/science.1113801

Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217. doi: 10.1002/jcc.540040211

Buchler NEG, Zuiderweg ERP, Wang H, Goldstein RA (1997) Protein heteronuclear NMR assignments using mean-field simulated annealing. J Magn Reson 125:34–42. doi: 10.1006/jmre.1997.1106

Carrara EA, Pagliari F, Nicolini C (1993) Neural networks for the peak picking of nuclear magnetic resonance spectra. Neural Netw 6:1023–1032

Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 104:9615–9620. doi: 10.1073/pnas.0610313104

Chatterjee A, Bhavesh NS, Panchal SC, Hosur RV (2002) A novel protocol based on HN(C)N for rapid resonance assignment in (15N, 13C) labeled proteins: implications to structural genomics. Biochem Biophys Res Commun 293:427–432. doi: 10.1016/S0006-291X(02)00240-1

Chen ZZ, Lin GH, Rizzi R, Wen JJ, Xu D, Xu Y et al (2005) More reliable protein NMR peak assignment via improved 2-interval scheduling. J Comput Biol 12:129–146. doi: 10.1089/cmb.2005.12.129

Choy WY, Sanctuary BC, Zhu G (1997) Using neural network predicted secondary structure information in automatic protein NMR assignment. J Chem Inf Comput Sci 37:1086–1094. doi: 10.1021/ci970012c

Coggins BE, Zhou P (2003) PACES: protein sequential assignment by computer-assisted exhaustive search. J Biomol NMR 26:93–111. doi: 10.1023/A:1023589029301

Corne SA, Johnson AP, Fisher J (1992) An artificial neural network for classifying cross peaks in two-dimensional NMR spectra. J Magn Reson 100:256–266

Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM et al (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179–5197. doi: 10.1021/ja00124a002

Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302. doi: 10.1023/A:1008392405740

Croft D, Kemmink J, Neidig KP, Oschkinat H (1997) Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques. J Biomol NMR 10:207–219. doi: 10.1023/A:1018329420659

Dancea F, Günther U (2005) Automated protein NMR structure determination using wavelet de-noised NOESY spectra. J Biomol NMR 33:139–152. doi: 10.1007/s10858-005-3093-1

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. doi: 10.1007/BF00197809

Delaglio F, Kontaxis G, Bax A (2000) Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J Am Chem Soc 122:2142–2143. doi: 10.1021/ja993603n

Duggan BM, Legge GB, Dyson HJ, Wright PE (2001) SANE (Structure assisted NOE evaluation): an automated model-based approach for NOE assignment. J Biomol NMR 19:321–329. doi: 10.1023/A:1011227824104

Eccles C, Güntert P, Billeter M, Wüthrich K (1991) Efficient analysis of protein 2D NMR spectra using the software package EASY. J Biomol NMR 1:111–130. doi: 10.1007/BF01877224

Eghbalnia HR, Bahrami A, Wang LY, Assadi A, Markley JL (2005) Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO). J Biomol NMR 32:219–233. doi: 10.1007/s10858-005-7944-6

Freeman R, Kupče E (2003) New methods for fast multidimensional NMR. J Biomol NMR 27:101–113. doi: 10.1023/A:1024960302926

Friedrichs MS, Mueller L, Wittekind M (1994) An automated procedure for the assignment of protein 1HN, 15N, 13Cα, 1Hα, 13Cβ and 1Hβ resonances. J Biomol NMR 4:703–726. doi: 10.1007/BF00404279

Garrett DS, Powers R, Gronenborn AM, Clore GM (1991) A common sense approach to peak picking two-, three- and four-dimensional spectra using automatic computer analysis of contour diagrams. J Magn Reson 95:214–220

Goddard TD, Kneller DG (2001) Sparky 3. University of California, San Francisco

Grishaev A, Llinás M (2002a) CLOUDS, a protocol for deriving a molecular proton density via NMR. Proc Natl Acad Sci USA 99:6707–6712. doi: 10.1073/pnas.082114199

Grishaev A, Llinás M (2002b) Protein structure elucidation from NMR proton densities. Proc Natl Acad Sci USA 99:6713–6718. doi: 10.1073/pnas.042114399

Gronwald W, Kalbitzer HR (2004) Automated structure determination of proteins by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 44:33–96. doi: 10.1016/j.pnmrs.2003.12.002

Gronwald W, Willard L, Jellard T, Boyko RE, Rajarathnam K, Wishart DS et al (1998) CAMRA: chemical shift based computer aided protein NMR assignments. J Biomol NMR 12:395–405. doi: 10.1023/A:1008321629308

Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J et al (2002) Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J Biomol NMR 23:271–287. doi: 10.1023/A:1020279503261

Güntert P (2003) Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectrosc 43:105–125. doi: 10.1016/S0079-6565(03)00021-9

Güntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278:353–378

Güntert P, Berndt KD, Wüthrich K (1993) The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. J Biomol NMR 3:601–606. doi: 10.1007/BF00174613

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. doi: 10.1006/jmbi.1997.1284

Güntert P, Salzmann M, Braun D, Wüthrich K (2000) Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J Biomol NMR 18:129–137. doi: 10.1023/A:1008318805889

Habeck M, Rieping W, Linge JP, Nilges M (2004) NOE assignment with ARIA 2.0: the nuts and bolts. Methods Mol Biol 278:379–402

Hare BJ, Prestegard JH (1994) Application of neural networks to automated assignment of NMR spectra of proteins. J Biomol NMR 4:35–46. doi: 10.1007/BF00178334

Herrmann T, Güntert P, Wüthrich K (2002a) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171–189. doi: 10.1023/A:1021614115432

Herrmann T, Güntert P, Wüthrich K (2002b) 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. doi: 10.1016/S0022-2836(02)00241-3

Hitchens TK, Lukin JA, Zhan YP, McCallum SA, Rule GS (2003) MONTE: an automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J Biomol NMR 25:1–9. doi: 10.1023/A:1021975923026

Huang YPJ, Moseley HNB, Baran MC, Arrowsmith C, Powers R, Tejero R et al (2005) An integrated platform for automated analysis of protein NMR structures. Methods Enzymol 394:111–141. doi: 10.1016/S0076-6879(05)94005-6

Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins. Struct Funct Bioinform 62:587–603. doi: 10.1002/prot.20820

Hung LH, Samudrala R (2006) An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. J Biomol NMR 36:189–198. doi: 10.1007/s10858-006-9082-1

Ikeya T, Yoshida H, Terauchi T, Kainosho M, Güntert P (2008) Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system. J Biomol NMR (in press)

Jee J, Güntert P (2003) Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. J Struct Funct Genomics 4:179–189. doi: 10.1023/A:1026122726574

Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278:313–352

Johnson BA, Blevins RA (1994) NMR View: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614. doi: 10.1007/BF00404272

Jung YS, Sharma M, Zweckstetter M (2004) Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings. Angew Chem Int Ed 43:3479–3481. doi: 10.1002/anie.200353588

Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, Güntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52–57. doi: 10.1038/nature04525

Kamisetty H, Bailey-Kellogg C, Pandurangan G (2006) An efficient randomized algorithm for contact-based NMR backbone resonance assignment. Bioinformatics 22:172–180. doi: 10.1093/bioinformatics/bti786

Keller RLJ (2004) Optimizing the process of nuclear magnetic resonance spectrum analysis and computer aided resonance assignment, PhD thesis. Institute of Molecular Biology and Biophysics. ETH, Zürich

Kjaer M, Andersen KV, Poulsen FM (1994) Automated and semiautomated analysis of homonuclear and heteronuclear multidimensional nuclear magnetic resonance spectra of proteins—the program PRONTO. Methods Enzymol 239:288–307. doi: 10.1016/S0076-6879(94)39010-X

Kleywegt GJ, Boelens R, Kaptein R (1990) A versatile approach toward the partially automatic recognition of cross peaks in 2D 1H NMR spectra. J Magn Reson 88:601–608

Kobayashi N, Iwahara J, Koshiba S, Tomizawa T, Tochio N, Güntert P et al (2007) KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J Biomol NMR 39:31–52. doi: 10.1007/s10858-007-9175-5

Koradi R, Billeter M, Engeli M, Güntert P, Wüthrich K (1998) Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J Magn Reson 135:288–297. doi: 10.1006/jmre.1998.1570

Koradi R, Billeter M, Güntert P (2000) Point-centered domain decomposition for parallel molecular dynamics simulation. Comput Phys Commun 124:139–147. doi: 10.1016/S0010-4655(99)00436-1

Kraulis PJ (1989) ANSIG: a program for the assignment of protein 1H 2D NMR spectra by interactive computer graphics. J Magn Reson 84:627–633

Kraulis PJ (1994) Protein three-dimensional structure determination and sequence-specific assignment of 13C-separated and 15N-separated NOE Data - a novel real-space ab-initio approach. J Mol Biol 243:696–718

Kumar A, Ernst RR, Wüthrich K (1980) A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton–proton cross-relaxation networks in biological macromolecules. Biochem Biophys Res Commun 95:1–6. doi: 10.1016/0006-291X(80)90695-6

Kuszewski J, Schwieters CD, Garrett DS, Byrd RA, Tjandra N, Clore GM (2004) Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments. J Am Chem Soc 126:6258–6273. doi: 10.1021/ja049786h

Leutner M, Gschwind RM, Liermann J, Schwarz C, Gemmecker G, Kessler H (1998) Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J Biomol NMR 11:31–43. doi: 10.1023/A:1008298226961

Li KB, Sanctuary BC (1997a) Automated resonance assignment of proteins using heteronuclear 3D NMR. 1. Backbone spin systems extraction and creation of polypeptides. J Chem Inf Comput Sci 37:359–366. doi: 10.1021/ci960045c

Li KB, Sanctuary BC (1997b) Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. J Chem Inf Comput Sci 37:467–477. doi: 10.1021/ci960372k

Lin HN, Wu KP, Chang JM, Sung TY, Hsu WL (2005) GANA: a genetic algorithm for NMR backbone resonance assignment. Nucleic Acids Res 33:4593–4601. doi: 10.1093/nar/gki768

Linge JP, Habeck M, Rieping W, Nilges M (2003a) ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19:315–316. doi: 10.1093/bioinformatics/19.2.315

Linge JP, Williams MA, Spronk CAEM, Bonvin AMJJ, Nilges M (2003b) Refinement of protein structures in explicit solvent. Proteins. Struct Funct Bioinformatics 50:496–506. doi: 10.1002/prot.10299

López-Méndez B, Güntert P (2006) Automated protein structure determination from NMR spectra. J Am Chem Soc 128:13112–13122. doi: 10.1021/ja061136l

López-Méndez B, Pantoja-Uceda D, Tomizawa T, Koshiba S, Kigawa T, Shirouzu M et al (2004) Letter to the Editor: NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana. J Biomol NMR 29:205–206

Luginbühl P, Güntert P, Billeter M, Wüthrich K (1996) The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. J Biomol NMR 8:136–146. doi: 10.1007/BF00211160

Lukin JA, Gove AP, Talukdar SN, Ho C (1997) Automated probabilistic method for assigning backbone resonances of (C-13, N-15)-labeled proteins. J Biomol NMR 9:151–166. doi: 10.1023/A:1018602220061

Macura S, Ernst RR (1980) Elucidation of cross relaxation in liquids by 2D NMR spectroscopy. Mol Phys 41:95–117. doi: 10.1080/00268978000102601

Malliavin TE, Rouh A, Delsuc MA, Lallemand JY (1992) Approche directe de la détermination de structures moléculaires à partir de l’effet Overhauser nucléaire. Comptes rendus de l’Academie des Sciences Serie II 315:653–659

Malmodin D, Papavoine CHM, Billeter M (2003) Fully automated sequence-specific resonance assignments of heteronuclear protein spectra. J Biomol NMR 27:69–79. doi: 10.1023/A:1024765212223

Masse JE, Keller R (2005) AutoLink: automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic. J Magn Reson 174:133–151. doi: 10.1016/j.jmr.2005.01.017

Masse JE, Keller R, Pervushin K (2006) SideLink: automated side-chain assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic. J Magn Reson 181:45–67. doi: 10.1016/j.jmr.2006.03.012

Meadows RP, Olejniczak ET, Fesik SW (1994) A computer-based protocol for semiautomated assignments and 3D structure determination of proteins. J Biomol NMR 4:79–96. doi: 10.1007/BF00178337

Meier BU, Bodenhausen G, Ernst RR (1984) Pattern recognition in two-dimensional NMR spectra. J Magn Reson 60:161–163

Meiler J, Baker D (2003) Rapid protein fold determination using unassigned NMR data. Proc Natl Acad Sci USA 100:15404–15409. doi: 10.1073/pnas.2434121100

Moseley HNB, Montelione GT (1999) Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol 9:635–642. doi: 10.1016/S0959-440X(99)00019-6

Moseley HNB, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Nucl Magn Reson Biol Macromol B 339:91–108

Moseley HNB, Riaz N, Aramini JM, Szyperski T, Montelione GT (2004) A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra. J Magn Reson 170:263–277. doi: 10.1016/j.jmr.2004.06.015

Mumenthaler C, Braun W (1995) Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. J Mol Biol 254:465–480. doi: 10.1006/jmbi.1995.0631

Mumenthaler C, Güntert P, Braun W, Wüthrich K (1997) Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J Biomol NMR 10:351–362. doi: 10.1023/A:1018383106236

Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB et al (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins. Struct Funct Bioinformatics 59:662–672. doi: 10.1002/prot.20408

Neidig KP, Saffrich R, Lorenz M, Kalbitzer HR (1990) Cluster analysis and multiplet pattern recognition in two-dimensional NMR spectra. J Magn Reson 89:543–552

Neidig KP, Geyer M, Gorler A, Antz C, Saffrich R, Beneicke W et al (1995) Aurelia, a program for computer-aided analysis of multidimensional NMR spectra. J Biomol NMR 6:255–270. doi: 10.1007/BF00197807

Neuhaus D, Williamson MP (1989) The nuclear Overhauser effect in structural and conformational analysis. VCH, Weinheim

Nilges M (1995) Calculation of protein structures with ambiguous distance restraints: automated assignment of ambiguous NOE crosspeaks and disulfide connectivities. J Mol Biol 245:645–660. doi: 10.1006/jmbi.1994.0053

Nilges M, Macias MJ, ODonoghue SI, Oschkinat H (1997) Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol 269:408–422. doi: 10.1006/jmbi.1997.1044

Olson JB, Markley JL (1994) Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package. J Biomol NMR 4:385–410. doi: 10.1007/BF00179348

Oshiro CM, Kuntz ID (1993) Application of distance geometry to the proton assignment problem. Biopolymers 33:107–115. doi: 10.1002/bip.360330110

Pantoja-Uceda D, López-Méndez B, Koshiba S, Inoue M, Kigawa T, Terada T et al (2005) Solution structure of the rhodanese homology domain At4g01050(175–295) from Arabidopsis thaliana. Protein Sci 14:224–230. doi: 10.1110/ps.041138705

Pfändler P, Bodenhausen G, Meier BU, Ernst RR (1985) Toward automated assignment of nuclear magnetic resonance spectra: pattern recognition in two-dimensional correlation spectra. Anal Chem 57:2510–2516. doi: 10.1021/ac00290a018

Prestegard JH, Mayer KL, Valafar H, Benison GC (2005) Determination of protein backbone structures from residual dipolar couplings. Methods Enzymol 394:175–209. doi: 10.1016/S0076-6879(05)94007-X

Pristovšek P, Rüterjans H, Jerala R (2002) Semiautomatic sequence-specific assignment of proteins based on the tertiary structure: the program st2nmr. J Comput Chem 23:335–340. doi: 10.1002/jcc.10011

Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M (2007) ARIA2: automated NOE assignment and data integration in NMR structure calculation. Bioinformatics 23:381–382. doi: 10.1093/bioinformatics/btl589

Rohl CA, Baker D (2002) De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc 124:2723–2729. doi: 10.1021/ja016880e

Rouh A, Louisjoseph A, Lallemand JY (1994) Bayesian signal extraction from noisy FT NMR spectra. J Biomol NMR 4:505–518. doi: 10.1007/BF00156617

Scott A, Pantoja-Uceda D, Koshiba S, Inoue M, Kigawa T, Terada T et al (2005) Solution structure of the Src homology 2 domain from the human feline sarcoma oncogene Fes. J Biomol NMR 31:357–361. doi: 10.1007/s10858-005-0946-6

Scott A, López-Méndez B, Güntert P (2006) Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra. Magn Reson Chem 44:S83–S88. doi: 10.1002/mrc.1813

Seavey BR, Farr EA, Westler WM, Markley JL (1991) A relational database for sequence-specific protein NMR data. J Biomol NMR 1:217–236. doi: 10.1007/BF01875516

Shen Y, Bax A (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38:289–302. doi: 10.1007/s10858-007-9166-6

Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G et al (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685–4690. doi: 10.1073/pnas.0800256105

Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268:209–225. doi: 10.1006/jmbi.1997.0959

Solomon I (1955) Relaxation processes in a system of two spins. Phys Rev 99:559–565. doi: 10.1103/PhysRev.99.559

Takeda M, Ikeya T, Güntert P, Kainosho M (2007) Automated structure determination of proteins with the SAIL-FLYA NMR method. Nat Protocols 2:2896–2902. doi: 10.1038/nprot.2007.423

Vitek O, Bailey-Kellogg C, Craig B, Kuliniewicz P, Vitek J (2005) Reconsidering complete search algorithms for protein backbone NMR assignment. Bioinformatics 21:230–236. doi: 10.1093/bioinformatics/bti1138

Vitek O, Bailey-Kellogg C, Craig B, Vitek J (2006) Inferential backbone assignment for sparse data. J Biomol NMR 35:187–208. doi: 10.1007/s10858-006-9027-8

Volk J, Herrmann T, Wüthrich K (2008) Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH. J Biomol NMR 41:127–138. doi: 10.1007/s10858-008-9243-5

Wang JY, Wang TZ, Zuiderweg ERP, Crippen GM (2005) CASA: an efficient automated assignment of protein mainchain NMR data using an ordered tree search algorithm. J Biomol NMR 33:261–279. doi: 10.1007/s10858-005-4079-8

Wishart DS, Sykes BD (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171–180. doi: 10.1007/BF00175245

Wu KP, Chang JM, Chen JB, Chang CF, Wu WJ, Huang TH et al (2006) RIBRA: an error-tolerant algorithm for the NMR backbone assignment problem. J Comput Biol 13:229–244. doi: 10.1089/cmb.2006.13.229

Xu J, Straus SK, Sanctuary BC, Trimble L (1993) Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and graph theory. J Chem Inf Comput Sci 33:668–682. doi: 10.1021/ci00015a004

Xu J, Straus SK, Sanctuary BC, Trimble L (1994) Use of fuzzy mathematics for complete automated assignment of peptide 1H 2D NMR spectra. J Magn Reson B 103:53–58. doi: 10.1006/jmrb.1994.1006

Xu Y, Xu D, Kim D, Olman V, Razumovskaya J, Jiang T (2002) Automated assignment of backbone NMR peaks using constrained bipartite matching. Comput Sci Eng 4:50–62

Xu YZ, Wang XX, Yang J, Vaynberg J, Qin J (2006) PASA: a program for automated protein NMR backbone signal assignment by pattern-filtering approach. J Biomol NMR 34:41–56. doi: 10.1007/s10858-005-5358-0

Zimmerman DE, Kulikowski CA, Huang YP, Feng WQ, Tashiro M, Shimotakahara S et al (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592–610. doi: 10.1006/jmbi.1997.1052