DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure.

[1]  A. Bax,et al.  TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts , 2009, Journal of biomolecular NMR.

[2]  Michele Vendruscolo,et al.  Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology. , 2009, The journal of physical chemistry. B.

[3]  S. P. Mielke,et al.  Characterization of protein secondary structure from NMR chemical shifts. , 2009, Progress in nuclear magnetic resonance spectroscopy.

[4]  Yaoqi Zhou,et al.  Improving the prediction accuracy of residue solvent accessibility and real‐value backbone torsion angles of proteins by guided‐learning through a two‐layer neural network , 2009, Proteins.

[5]  A. Bax,et al.  De novo protein structure generation from incomplete chemical shift assignments , 2009, Journal of biomolecular NMR.

[6]  Paul Robustelli,et al.  Determination of protein structures in the solid state from NMR chemical shifts. , 2008, Structure.

[7]  D. Wishart,et al.  CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data , 2008, Nucleic Acids Res..

[8]  Christian Cole,et al.  The Jpred 3 secondary structure prediction server , 2008, Nucleic Acids Res..

[9]  M. Vannucci,et al.  Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space. , 2008, Journal of molecular biology.

[10]  Michael Nilges,et al.  ISD: a software package for Bayesian NMR structure calculation , 2008, Bioinform..

[11]  Oliver F. Lange,et al.  Consistent blind protein structure generation from NMR chemical shift data , 2008, Proceedings of the National Academy of Sciences.

[12]  M. Nilges,et al.  3D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints. , 2008, Journal of the American Chemical Society.

[13]  A. Bax,et al.  Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology , 2007, Journal of biomolecular NMR.

[14]  Michele Vendruscolo,et al.  Protein structure determination from NMR chemical shifts , 2007, Proceedings of the National Academy of Sciences.

[15]  David S. Wishart,et al.  The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts , 2007, Nucleic Acids Res..

[16]  David S Wishart,et al.  NMR: prediction of protein flexibility , 2006, Nature Protocols.

[17]  Mark Berjanskii,et al.  Accurate prediction of protein torsion angles using chemical shifts and sequence homology , 2006, Magnetic resonance in chemistry : MRC.

[18]  David S. Wishart,et al.  PREDITOR: a web server for predicting protein torsion angle restraints , 2006, Nucleic Acids Res..

[19]  A. Bohm,et al.  Crystal Structure of the Simian Virus 40 Large T-Antigen Origin-Binding Domain , 2006, Journal of Virology.

[20]  David S Wishart,et al.  A simple method to predict protein flexibility using secondary chemical shifts. , 2005, Journal of the American Chemical Society.

[21]  Thomas M. Cover,et al.  Elements of Information Theory , 2005 .

[22]  Bosco K. Ho,et al.  The Ramachandran plots of glycine and pre-proline , 2005, BMC Structural Biology.

[23]  Miron Livny,et al.  RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank , 2005, Proteins.

[24]  Wayne Boucher,et al.  The CCPN data model for NMR spectroscopy: Development of a software pipeline , 2005, Proteins.

[25]  J. Markley,et al.  Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements , 2005, Journal of biomolecular NMR.

[26]  Bosco K. Ho,et al.  Revisiting the Ramachandran plot: Hard‐sphere repulsion, electrostatics, and H‐bonding in the α‐helix , 2003, Protein science : a publication of the Protein Society.

[27]  Gert Vriend,et al.  Quantitative evaluation of experimental NMR restraints. , 2003, Journal of the American Chemical Society.

[28]  D. Wishart,et al.  Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts , 2003, Journal of biomolecular NMR.

[29]  Jun Zhu,et al.  BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank , 2003, Journal of biomolecular NMR.

[30]  David S Wishart,et al.  RefDB: A database of uniformly referenced protein chemical shifts , 2003, Journal of biomolecular NMR.

[31]  Ian W. Davis,et al.  Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.

[32]  Ram Samudrala,et al.  Accurate and automated classification of protein secondary structure with PsiCSI , 2003, Protein science : a publication of the Protein Society.

[33]  Oleg Jardetzky,et al.  Probability‐based protein secondary structure identification using combined NMR chemical‐shift data , 2002, Protein science : a publication of the Protein Society.

[34]  D. Case,et al.  Use of chemical shifts in macromolecular structure determination. , 2002, Methods in enzymology.

[35]  C. A. Andersen,et al.  Continuum secondary structure captures protein flexibility. , 2002, Structure.

[36]  B. Rost.  Review: protein secondary structure prediction continues to rise. , 2001, Journal of structural biology.

[37]  P E Wright,et al.  Sequence-dependent correction of random coil NMR chemical shifts. , 2001, Journal of the American Chemical Society.

[38]  H. Dyson,et al.  NMR structural and dynamic characterization of the acid-unfolded state of apomyoglobin provides insights into the early events in protein folding. , 2001, Biochemistry.

[39]  H. Jane Dyson,et al.  Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView , 2000, Journal of biomolecular NMR.

[40]  A. Bax,et al.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology , 1999, Journal of biomolecular NMR.

[41]  Mitsuo Iwadate,et al.  Cα and Cβ Carbon-13 Chemical Shifts in Proteins From an Empirical Database , 1999 .

[42]  N. Sin,et al.  Deuterium Isotope Effects on13C NMR Chemical Shifts of Amides , 1997 .

[43]  D. Sanford,et al.  Solution structure of the origin DNA-binding domain of SV40 T-antigen , 1996, Nature Structural Biology.

[44]  K. Constantine,et al.  Characterization of the three-dimensional solution structure of human profilin: proton, carbon-13, and nitrogen-15 NMR assignments and global folding pattern , 1993 .

[45]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[46]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[47]  W. D. Phillips,et al.  Manifestations of the tertiary structures of proteins in high-frequency nuclear magnetic resonance. , 1967, Journal of the American Chemical Society.

[48]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.

[49]  K. Chary,et al.  An efficient method for secondary structure determination in polypeptides by NMR , 2008 .

[50]  David S. Wishart,et al.  Application of the random coil index to studying protein flexibility , 2008, Journal of biomolecular NMR.

[51]  Yutaka Kuroda,et al.  Improvement of domain linker prediction by incorporating loop-length-dependent characteristics. , 2006, Biopolymers.

[52]  M. Tribus,et al.  Probability theory: the logic of science , 2005 .

[53]  Vladimir N Uversky,et al.  What does it mean to be natively unfolded? , 2002, European journal of biochemistry.

[54]  László Szilágyi,et al.  Chemical shifts in proteins come of age , 1995 .

[55]  B D Sykes,et al.  Chemical shifts as a tool for structure determination. , 1994, Methods in enzymology.

[56]  Jianhua Lin,et al.  Divergence measures based on the Shannon entropy , 1991, IEEE Trans. Inf. Theory.

[57]  N. Sergeev,et al.  Negative linear deuterium isotope shift for13C in iodoform , 1987 .

[58]  H. Berman,et al.  The Protein Data Bank. , 2002, Acta crystallographica. Section D, Biological crystallography.