CSI 2.0: a significantly improved version of the Chemical Shift Index

[1]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[2]  A. Bax,et al.  Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks , 2013, Journal of Biomolecular NMR.

[3]  David Baker,et al.  Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. , 2013, Annual review of biophysics.

[4]  Carlo Camilloni,et al.  Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts. , 2012, Biochemistry.

[5]  A. Bax,et al.  Identification of helix capping and β-turn motifs from NMR chemical shifts , 2012, Journal of biomolecular NMR.

[6]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[7]  Johannes Söding,et al.  Protein sequence comparison and fold recognition: progress and good-practice benchmarking. , 2011, Current opinion in structural biology.

[8]  Simon W. Ginzinger,et al.  SHIFTX2: significantly improved protein chemical shift prediction , 2011, Journal of biomolecular NMR.

[9]  David S Wishart,et al.  Interpreting protein chemical shift data. , 2011, Progress in nuclear magnetic resonance spectroscopy.

[10]  Tim J Stevens,et al.  DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure. , 2010, Journal of magnetic resonance.

[11]  D. Baker,et al.  De novo structure generation using chemical shifts for proteins with high‐sequence identity but different folds , 2010, Protein science : a publication of the Protein Society.

[12]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[13]  P. Alexander,et al.  A minimal sequence code for switching protein structure and function , 2009, Proceedings of the National Academy of Sciences.

[14]  A. Bornot,et al.  Analysis of loop boundaries using different local structure assignment methods , 2009, Protein science : a publication of the Protein Society.

[15]  A. Dunker,et al.  Predicting intrinsic disorder in proteins: an overview , 2009, Cell Research.

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

[17]  David S. Wishart,et al.  GeNMR: a web server for rapid NMR-based protein structure determination , 2009, Nucleic Acids Res..

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

[19]  D. Baker,et al.  De novo protein structure generation from incomplete chemical shift assignments , 2009, Journal of biomolecular NMR.

[20]  Max Kuhn,et al.  Building Predictive Models in R Using the caret Package , 2008 .

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

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

[23]  A Keith Dunker,et al.  Assessing secondary structure assignment of protein structures by using pairwise sequence‐alignment benchmarks , 2008, Proteins.

[24]  Miron Livny,et al.  BioMagResBank , 2007, Nucleic Acids Res..

[25]  Hamid Pezeshk,et al.  Impact of residue accessible surface area on the prediction of protein secondary structures , 2008, BMC Bioinformatics.

[26]  Michael Andrec,et al.  A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing , 2007, Proteins.

[27]  John L Markley,et al.  Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins , 2007, Journal of biomolecular NMR.

[28]  Woei-Jer Chuang,et al.  2DCSi: identification of protein secondary structure and redox state using 2D cluster analysis of NMR chemical shifts , 2007, Journal of biomolecular NMR.

[29]  David S. Wishart,et al.  Improving the accuracy of protein secondary structure prediction using structural alignment , 2006, BMC Bioinformatics.

[30]  R. Fesinmeyer,et al.  Chemical Shifts Provide Fold Populations and Register of β Hairpins and β Sheets , 2005 .

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

[32]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[33]  Aleksey A. Porollo,et al.  Combining prediction of secondary structure and solvent accessibility in proteins , 2005, Proteins.

[34]  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.

[35]  Kurt Hornik,et al.  kernlab - An S4 Package for Kernel Methods in R , 2004 .

[36]  David S. Wishart,et al.  VADAR: a web server for quantitative evaluation of protein structure quality , 2003, Nucleic Acids Res..

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

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

[39]  H Oschkinat,et al.  Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts , 2003, Journal of biomolecular NMR.

[40]  O. Jardetzky,et al.  Investigation of the neighboring residue effects on protein chemical shifts. , 2002, Journal of the American Chemical Society.

[41]  W. S. Valdar,et al.  Scoring residue conservation , 2002, Proteins.

[42]  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.

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

[44]  Marc A. Martí-Renom,et al.  EVA: continuous automatic evaluation of protein structure prediction servers , 2001, Bioinform..

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

[46]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[47]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[48]  B. Rost,et al.  A modified definition of Sov, a segment‐based measure for protein secondary structure prediction assessment , 1999, Proteins.

[49]  D. T. Jones,et al.  Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure , 1999, Proteins.

[50]  R. Varadarajan,et al.  Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. , 1998, Biochemistry.

[51]  D. Wishart,et al.  Protein chemical shift analysis: a practical guide. , 1998, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[52]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[53]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[54]  D. Wishart,et al.  The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data , 1994, Journal of biomolecular NMR.

[55]  B. Rost,et al.  Redefining the goals of protein secondary structure prediction. , 1994, Journal of molecular biology.

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

[57]  F. Richards,et al.  The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. , 1992, Biochemistry.

[58]  K. Wüthrich.  Protein structure determination in solution by NMR spectroscopy. , 1990, The Journal of biological chemistry.

[59]  K. Wüthrich.  NMR of proteins and nucleic acids , 1988 .

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

[61]  S. P. Mielkea,et al.  An evaluation of chemical shift index-based secondary structure determination in proteins : Influence of random coil chemical shifts ∗ , 2022 .