TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts (original) (raw)
References
Ando I, Kameda T, Asakawa N, Kuroki S, Kurosu H (1998) Structure of peptides and polypeptides in the solid state as elucidated by NMR chemical shift. J Mol Struct 441:213–230 ArticleADS Google Scholar
Andreassen H, Bohr H, Bohr J, Brunak S, Bugge T, Cotterill RMJ, Jacobsen C, Kusk P, Lautrop B, Petersen SB, Saermark T, Ulrich K (1990) Analysis of the secondary structure of the human immunodeficiency virus (HIV) proteins p17, gp120, and gp41 by computer modeling based on neural network methods. J Acquir Immune Defic Syndr 3:615–622 Google Scholar
Asakura T, Demura M, Date T, Miyashita N, Ogawa K, Williamson MP (1997) NMR study of silk I structure of Bombyx mori silk fibroin with N-15- and C-13-NMR chemical shift contour plots. Biopolymers 41:193–203 Article Google Scholar
Berjanskii MV, Wishart DS (2005) A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc 127:14970–14971 Article Google Scholar
Berjanskii MV, Wishart DS (2008) Application of the random coil index to studying protein flexibility. J Biomol NMR 40:31–48 Article Google Scholar
Billeter M, Wagner G, Wuthrich K (2008) Solution NMR structure determination of proteins revisited. J Biomol NMR 42:155–158 Article Google Scholar
Cai M, Huang Y, Zheng R, Wei SQ, Ghirlando R, Lee MS, Craigie R, Gronenborn AM, Clore GM (1998) Solution structure of the cellular factor BAF responsible for protecting retroviral DNA from autointegration. Nat Struct Biol 5:903–909 Article Google Scholar
Case DA (1995) Calibration of ring-current effects in proteins and nucleic acids. J Biomol NMR 6:341–346 Article Google Scholar
Castellani F, van Rossum BJ, Diehl A, Rehbein K, Oschkinat H (2003) Determination of solid-state NMR structures of proteins by means of three-dimensional N-15-C-13-C-13 dipolar correlation spectroscopy and chemical shift analysis. Biochemistry 42:11476–11483 Article Google Scholar
Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 104:9615–9620 ArticleADS Google Scholar
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 Google Scholar
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 Article Google Scholar
Czinki E, Csaszar AG (2007) Empirical isotropic chemical shift surfaces. J Biomol NMR 38:269–287 Article Google Scholar
Grishaev A, Tugarinov V, Kay LE, Trewhella J, Bax A (2008) Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints. J Biomol NMR 40:95–106 Article Google Scholar
Haigh CW, Mallion RB (1979) Ring current theories in nuclear magnetic resonance. Prog Nucl Magn Reson Spectrosc 13:303–344 Article Google Scholar
Hare BJ, Prestegard JH (1994) Application of neural networks to automated assignment of NMR spectra of proteins. J Biomol NMR 4:35–46 Article Google Scholar
Huang K, Andrec M, Heald S, Blake P, Prestegard JH (1997) Performance of a neural-network-based determination of amino acid class and secondary structure from H-1-N-15 NMR data. J Biomol NMR 10:45–52 Article Google Scholar
Hung LH, Samudrala R (2003) Accurate and automated classification of protein secondary structure with PsiCSI. Protein Sci 12:288–295 Article Google Scholar
Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202 Article Google Scholar
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637 Article Google Scholar
Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40:153–155 Article Google Scholar
Meiler J (2003) PROSHIFT: protein chemical shift prediction using artificial neural networks. J Biomol NMR 26:25–37 Article Google Scholar
Moon S, Case DA (2007) A new model for chemical shifts of amide hydrogens in proteins. J Biomol NMR 38:139–150 Article Google Scholar
Neal S, Nip AM, Zhang HY, Wishart DS (2003) Rapid and accurate calculation of protein H-1, C-13 and N-15 chemical shifts. J Biomol NMR 26:215–240 Article Google Scholar
Neal S, Berjanskii M, Zhang HY, Wishart DS (2006) Accurate prediction of protein torsion angles using chemical shifts and sequence homology. Magn Reson Chem 44:S158–S167 Article Google Scholar
Parsons LM, Grishaev A, Bax A (2008) The periplasmic domain of TolR from haemophilus influenzae forms a dimer with a large hydrophobic groove: NMR solution structure and comparison to SAXS data. Biochemistry 47:3131–3142 Article Google Scholar
Pons JL, Delsuc MA (1999) RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins. J Biomol NMR 15:15–26 Article Google Scholar
Ramirez BE, Voloshin ON, Camerini-Otero RD, Bax A (2000) Solution structure of DinI provides insight into its mode of RecA inactivation. Protein Sci 9:2161–2169 Article Google Scholar
Rost B, Sander C (1993) Prediction of protein secondary structure at better than 70 percent accuracy. J Mol Biol 232:584–599 Article Google Scholar
Saito H (1986) Conformation-dependent C13 chemical shifts—a new means of conformational characterization as obtained by high resolution solid state C13 NMR. Magn Reson Chem 24:835–852 Article Google Scholar
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 Article Google Scholar
Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu GH, Eletsky A, Wu YB, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685–4690 ArticleADS Google Scholar
Shen Y, Vernon R, Baker D, Bax A (2009) De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 43:63–78 Article Google Scholar
Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and Cα and Cβ 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490–5492 Article Google Scholar
Tugarinov V, Choy WY, Orekhov VY, Kay LE (2005) Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc Natl Acad Sci USA 102:622–627 ArticleADS Google Scholar
Ulmer TS, Ramirez BE, Delaglio F, Bax A (2003) Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. J Am Chem Soc 125:9179–9191 Article Google Scholar
Vila JA, Villegas ME, Baldoni HA, Scheraga HA (2007) Predicting C-13(alpha) chemical shifts for validation of protein structures. J Biomol NMR 38:221–235 Article Google Scholar
Vila JA, Aramini JM, Rossi P, Kuzin A, Su M, Seetharaman J, Xiao R, Tong L, Montelione GT, Scheraga HA (2008) Quantum chemical C-13(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc Natl Acad Sci USA 105:14389–14394 ArticleADS Google Scholar
Villegas ME, Vila JA, Scheraga HA (2007) Effects of side-chain orientation on the C-13 chemical shifts of antiparallel beta-sheet model peptides. J Biomol NMR 37:137–146 Article Google Scholar
Wagner G, Pardi A, Wuthrich K (1983) Hydrogen-bond length and H-1-Nmr chemical-shifts in proteins. J Am Chem Soc 105:5948–5949 Article Google Scholar
Wang YJ, Jardetzky O (2002) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852–861 Article Google Scholar
Williamson MP, Asakura T (1993) Empirical comparisons of models for chemical-shift calculation in proteins. J Magn Reson B 101:63–71 Article Google Scholar
Williamson MP, Kikuchi J, Asakura T (1995) Application of H1 NMR chemical shifts to measure the quality of protein structures. J Mol Biol 247:541–546 Google Scholar
Wishart DS, Sykes BD, Richards FM (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222:311–333 Article Google Scholar
Wishart DS, Sykes BD, Richards FM (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31:1647–1651 Article Google Scholar
Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G (2008) CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res 36:496–502 Article Google Scholar
Xu XP, Case DA (2001) Automated prediction of N-15, C-13(alpha), C-13(beta) and C-13′ chemical shifts in proteins using a density functional database. J Biomol NMR 21:321–333 Article Google Scholar