Secondary structure prediction

Abstract Information about the structure and function of a protein are encoded in its amino acid sequence. Continued progress in sequencing increasingly explodes the number of proteins for which the sequences are known but little other knowledge exists. After database searches through alignments, protein secondary structure predictions might be the most fundamental second step in finding out anything about those sequences. Secondary structure predictions can help in expert annotations and are used as input for many automated annotation tools. Today’s top prediction methods reach high levels of performance at relatively little computational costs.

[1]  B. Rost,et al.  Improved prediction of protein secondary structure by use of sequence profiles and neural networks. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Patrick Aloy,et al.  Predictions without templates: New folds, secondary structure, and contacts in CASP5 , 2003, Proteins.

[3]  D. Kihara.  The effect of long‐range interactions on the secondary structure formation of proteins , 2005, Protein science : a publication of the Protein Society.

[4]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[5]  P. Y. Chou,et al.  Prediction of protein conformation. , 1974, Biochemistry.

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

[7]  P. Y. Chou,et al.  Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. , 1974, Biochemistry.

[8]  Dmitrij Frishman,et al.  STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins , 2004, Nucleic Acids Res..

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

[10]  L. Pauling,et al.  Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets. , 1951, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. Gibrat,et al.  GOR method for predicting protein secondary structure from amino acid sequence. , 1996, Methods in enzymology.

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

[13]  C. Sander,et al.  Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.

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

[15]  Leszek Rychlewski,et al.  LiveBench‐8: The large‐scale, continuous assessment of automated protein structure prediction , 2005, Protein science : a publication of the Protein Society.

[16]  B. Rost,et al.  Combining evolutionary information and neural networks to predict protein secondary structure , 1994, Proteins.

[17]  R. King,et al.  Identification and application of the concepts important for accurate and reliable protein secondary structure prediction , 1996, Protein science : a publication of the Protein Society.

[18]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[19]  Bernard F. Buxton,et al.  Secondary structure prediction with support vector machines , 2003, Bioinform..

[20]  A. Szent-Gyorgyi,et al.  Role of proline in polypeptide chain configuration of proteins. , 1957, Science.

[21]  G J Barton,et al.  Evaluation and improvement of multiple sequence methods for protein secondary structure prediction , 1999, Proteins.

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

[23]  J. Gibrat,et al.  Protein secondary structure assignment revisited: a detailed analysis of different assignment methods , 2005, BMC Structural Biology.

[24]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[25]  Volker A. Eyrich,et al.  EVA: Large‐scale analysis of secondary structure prediction , 2001, Proteins.

[26]  Pierre Baldi,et al.  Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles , 2002, Proteins.

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

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

[29]  R. Casadio,et al.  Predictions of protein segments with the same aminoacid sequence and different secondary structure: A benchmark for predictive methods , 2000, Proteins.

[30]  K Fidelis,et al.  A large‐scale experiment to assess protein structure prediction methods , 1995, Proteins.

[31]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[32]  K-L Ting,et al.  Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence , 2002, Proteins.

[33]  G J Barton,et al.  Application of multiple sequence alignment profiles to improve protein secondary structure prediction , 2000, Proteins.

[34]  B. Rost,et al.  Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.

[35]  Geoffrey J. Barton,et al.  JPred : a consensus secondary structure prediction server , 1999 .

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

[37]  A A Salamov,et al.  Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. , 1995, Journal of molecular biology.