Protein structure prediction in the postgenomic era.

[1]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[2]  John P. Overington,et al.  Environment‐specific amino acid substitution tables: Tertiary templates and prediction of protein folds , 1992, Protein science : a publication of the Protein Society.

[3]  D. T. Jones,et al.  A new approach to protein fold recognition , 1992, Nature.

[4]  S. Bryant,et al.  An empirical energy function for threading protein sequence through the folding motif , 1993, Proteins.

[5]  C Sander,et al.  Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. , 1993, Journal of molecular biology.

[6]  David T. Jones,et al.  Protein superfamilles and domain superfolds , 1994, Nature.

[7]  M J Sippl,et al.  Progress in fold recognition , 1995, Proteins.

[8]  S. Eddy.  Hidden Markov models. , 1996, Current opinion in structural biology.

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

[10]  D. Fischer,et al.  Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[12]  J. Thornton,et al.  Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites , 1997, Protein science : a publication of the Protein Society.

[13]  David C. Jones,et al.  Progress in protein structure prediction. , 1997, Current opinion in structural biology.

[14]  David T. Jones.  Successful ab initio prediction of the tertiary structure of NK‐lysin using multiple sequences and recognized supersecondary structural motifs , 1997, Proteins.

[15]  A G Murzin,et al.  Distant homology recognition using structural classification of proteins , 1997, Proteins.

[16]  J Skolnick,et al.  Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. , 1998, Journal of molecular biology.

[17]  S. Kim,et al.  Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[18]  C. Chothia,et al.  Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[19]  A. Godzik,et al.  Fold and function predictions for Mycoplasma genitalium proteins. , 1998, Folding & design.

[20]  R. Grandori.  Systematic fold recognition analysis of the sequences encoded by the genome of Mycoplasma pneumoniae. , 1998, Protein engineering.

[21]  P Bork,et al.  Homology-based fold predictions for Mycoplasma genitalium proteins. , 1998, Journal of molecular biology.

[22]  Fan Yang,et al.  Crystal structure of Escherichia coli HdeA , 1998, Nature Structural Biology.

[23]  J. Skolnick,et al.  Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. , 1998, Journal of molecular biology.

[24]  M J Sternberg,et al.  Supersites within superfolds. Binding site similarity in the absence of homology. , 1998, Journal of molecular biology.

[25]  P. Bork,et al.  Predicting functions from protein sequences—where are the bottlenecks? , 1998, Nature Genetics.

[26]  C. Orengo,et al.  Protein folds and functions. , 1998, Structure.

[27]  L Shapiro,et al.  The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science. , 1998, Structure.

[28]  J L Sussman,et al.  Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. , 1998, Acta crystallographica. Section D, Biological crystallography.

[29]  C A Orengo,et al.  Genome analysis: Assigning protein coding regions to three‐dimensional structures , 1999 .

[30]  T. Alwyn Jones,et al.  CASP3 comparative modeling evaluation , 1999, Proteins.

[31]  Frances M. G. Pearl,et al.  Protein folds, functions and evolution. , 1999, Journal of molecular biology.

[32]  Richard Bonneau,et al.  Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.

[33]  A. Liwo,et al.  Calculation of protein conformation by global optimization of a potential energy function , 1999, Proteins.

[34]  David S. Eisenberg,et al.  Finding families for genomic ORFans , 1999, Bioinform..

[35]  Roland L. Dunbrack,et al.  Comparative modeling of CASP3 targets using PSI‐BLAST and SCWRL , 1999, Proteins.

[36]  K. Volz.  A test case for structure‐based functional assignment: The 1.2 Å crystal structure of the yjgF gene product from Escherichia coli , 2008, Protein science : a publication of the Protein Society.

[37]  D. Fischer.  Modeling three‐dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence‐derived predictions , 1999, Proteins.

[38]  D. Eisenberg,et al.  A combined algorithm for genome-wide prediction of protein function , 1999, Nature.

[39]  S. Cebrat,et al.  Total number of coding open reading frames in the yeast genome , 1999, Yeast.

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

[41]  M Gerstein,et al.  Advances in structural genomics. , 1999, Current opinion in structural biology.

[42]  M. Gerstein,et al.  The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. , 1999, Journal of molecular biology.

[43]  David C. Jones,et al.  GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.

[44]  Andrej Sali,et al.  Comparative Protein Structure Modeling in Genomics , 1999 .

[45]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[46]  D Fischer,et al.  CAFASP‐1: Critical assessment of fully automated structure prediction methods , 1999, Proteins.

[47]  Steven E. Brenner,et al.  The PRESAGE database for structural genomics , 1999, Nucleic Acids Res..

[48]  A. Godzik,et al.  Functional insights from structural predictions: Analysis of the Escherichia coli genome , 2008, Protein science : a publication of the Protein Society.

[49]  Declan Butler.  IBM promises scientists 500-fold leap in supercomputing power… , 1999, Nature.

[50]  Declan Butler.  …and a chance to tackle protein structure , 1999, Nature.

[51]  S E Brenner,et al.  Distribution of protein folds in the three superkingdoms of life. , 1999, Genome research.

[52]  T J Hubbard.  RMS/Coverage graphs: A qualitative method for comparing three‐dimensional protein structure predictions , 1999, Proteins.

[53]  M J Sternberg,et al.  Model building by comparison at CASP3: Using expert knowledge and computer automation , 1999, Proteins.