Fold predictions for bacterial genomes.
暂无分享,去创建一个
L Rychlewski | A Godzik | A. Godzik | L. Rychlewski | B. Zhang | K. Pawłowski | B Zhang | K Pawlowski | B. Zhang | B. Zhang | Baohong Zhang
[1] G Schneider,et al. Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network. , 2000, Protein engineering.
[2] S. Henikoff,et al. Drosophila genomic sequence annotation using the BLOCKS+ database. , 2000, Genome research.
[3] W A Koppensteiner,et al. Characterization of novel proteins based on known protein structures. , 2000, Journal of molecular biology.
[4] B. Rost,et al. Protein structures sustain evolutionary drift. , 1997, Folding & design.
[5] A. Krogh,et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.
[6] Liam J. McGuffin,et al. The PSIPRED protein structure prediction server , 2000, Bioinform..
[7] Richard H. Lathrop,et al. Current Limitations to Protein Threading Approaches , 1997, J. Comput. Biol..
[8] M J Sternberg,et al. Supersites within superfolds. Binding site similarity in the absence of homology. , 1998, Journal of molecular biology.
[9] M. Gerstein. Patterns of protein‐fold usage in eight microbial genomes: A comprehensive structural census , 1998, Proteins.
[10] 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.
[11] A. Godzik,et al. Functional insights from structural predictions: Analysis of the Escherichia coli genome , 2008, Protein science : a publication of the Protein Society.
[12] A. Godzik,et al. Fold and function predictions for Mycoplasma genitalium proteins. , 1998, Folding & design.
[13] W A Koppensteiner,et al. An attempt to analyse progress in fold recognition from CASP1 to CASP3 , 1999, Proteins.
[14] M. Riley. Systems for categorizing functions of gene products. , 1998, Current Opinion in Structural Biology.
[15] C A Smith,et al. Active site comparisons highlight structural similarities between myosin and other P-loop proteins. , 1996, Biophysical journal.
[16] Roland L. Dunbrack,et al. Genomic Fold Assignment and Rational Modeling of Proteins of Biological Interest , 2000, ISMB.
[17] R. King,et al. Accurate Prediction of Protein Functional Class From Sequence in the Mycobacterium Tuberculosis and Escherichia Coli Genomes Using Data Mining , 2000, Yeast.
[18] Obradovic,et al. Predicting Protein Disorder for N-, C-, and Internal Regions. , 1999, Genome informatics. Workshop on Genome Informatics.
[19] A. Sali,et al. Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.
[20] H. Dyson,et al. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. , 1999, Journal of molecular biology.
[21] Monica Riley,et al. Genes and proteins of Escherichia coli (GenProtEc) , 1996, Nucleic Acids Res..
[22] Stephen H. Bryant,et al. Domain size distributions can predict domain boundaries , 2000, Bioinform..
[23] J M Thornton,et al. Using the CATH domain database to assign structures and functions to the genome sequences. , 2000, Biochemical Society transactions.
[24] 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.
[25] P D Karp,et al. What we do not know about sequence analysis and sequence databases. , 1998, Bioinformatics.
[26] M. Helmer-Citterich,et al. Three-dimensional profiles: a new tool to identify protein surface similarities. , 1998, Journal of molecular biology.
[27] D Fischer,et al. Predicting structures for genome proteins. , 1999, Current opinion in structural biology.
[28] D. Haussler,et al. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. , 1998, Journal of molecular biology.
[29] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[30] A. Godzik,et al. Topology fingerprint approach to the inverse protein folding problem. , 1992, Journal of molecular biology.
[31] Annabel E. Todd,et al. From structure to function: Approaches and limitations , 2000, Nature Structural Biology.
[32] L Rychlewski,et al. From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions , 1999, Protein science : a publication of the Protein Society.
[33] S. Jones,et al. Analysis of protein-protein interaction sites using surface patches. , 1997, Journal of molecular biology.
[34] A Bairoch,et al. Protein annotation: detective work for function prediction. , 1998, Trends in genetics : TIG.
[35] D. T. Jones. Protein structure prediction in the postgenomic era. , 2000, Current opinion in structural biology.
[36] Mark Borodovsky,et al. The complete genome sequence of the gastric pathogen Helicobacter pylori , 1997, Nature.
[37] S H Kim,et al. Assignment of folds for proteins of unknown function in three microbial genomes. , 1998, Microbial & comparative genomics.
[38] 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.
[39] F E Cohen,et al. Protein misfolding and prion diseases. , 1999, Journal of molecular biology.
[40] Michael Y. Galperin,et al. Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs) , 2000, Genome Biology.
[41] M. Gerstein,et al. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. , 2000, Journal of molecular biology.
[42] Michael Y. Galperin,et al. Analogous enzymes: independent inventions in enzyme evolution. , 1998, Genome research.
[43] S. Pietrokovski. Searching databases of conserved sequence regions by aligning protein multiple-alignments. , 1996, Nucleic acids research.
[44] Richard Bonneau,et al. Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.
[45] A. Sali,et al. Protein structure modeling for structural genomics , 2000, Nature Structural Biology.
[46] A. Godzik,et al. Sensitive sequence comparison as protein function predictor. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[47] David S. Eisenberg,et al. Finding families for genomic ORFans , 1999, Bioinform..
[48] C. Orengo,et al. Protein folds and functions. , 1998, Structure.
[49] Amos Bairoch,et al. The ENZYME data bank in 1999 , 1999, Nucleic Acids Res..
[50] P. Romero,et al. Sequence complexity of disordered protein , 2001, Proteins.
[51] K Wüthrich,et al. NMR solution structure of the human prion protein. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[52] E V Koonin,et al. Protein fold recognition using sequence profiles and its application in structural genomics. , 2000, Advances in protein chemistry.
[53] A. D. McLachlan,et al. Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[54] G J Barton,et al. Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility. , 1994, Journal of molecular biology.
[55] M Gerstein,et al. Advances in structural genomics. , 1999, Current opinion in structural biology.
[56] Golan Yona,et al. Towards a Complete Map of the Protein Space Based on a Unified Sequence and Structure Analysis of All Known Proteins , 2000, ISMB.
[57] E. Marcotte,et al. Computational genetics: finding protein function by nonhomology methods. , 2000, Current opinion in structural biology.
[58] Yan P. Yuan,et al. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. , 2000, Nucleic acids research.
[59] David C. Jones,et al. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.
[60] R. Russell,et al. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. , 1998, Journal of molecular biology.
[61] Stephen K. Burley,et al. An overview of structural genomics , 2000, Nature Structural Biology.
[62] D Fischer,et al. The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2. , 2000, Protein engineering.
[63] F. Cohen,et al. An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.
[64] Fan Yang,et al. Crystal structure of Escherichia coli HdeA , 1998, Nature Structural Biology.
[65] Leszek Rychlewski,et al. Improving the quality of twilight‐zone alignments , 2000, Protein science : a publication of the Protein Society.
[66] A. Godzik,et al. Comparison of sequence profiles. Strategies for structural predictions using sequence information , 2008, Protein science : a publication of the Protein Society.
[67] J Moult,et al. From fold to function. , 2000, Current opinion in structural biology.
[68] P Bork,et al. Homology-based fold predictions for Mycoplasma genitalium proteins. , 1998, Journal of molecular biology.
[69] R. Fleischmann,et al. The Minimal Gene Complement of Mycoplasma genitalium , 1995, Science.
[70] A. Valencia,et al. Practical limits of function prediction , 2000, Proteins.
[71] H. Kessler,et al. The solution structure of VAT-N reveals a ‘missing link’ in the evolution of complex enzymes from a simple βαββ element , 1999, Current Biology.
[72] D Fischer,et al. CAFASP‐1: Critical assessment of fully automated structure prediction methods , 1999, Proteins.
[73] A. Lupas,et al. Predicting coiled coils from protein sequences , 1991, Science.
[74] D. Eisenberg,et al. Protein function in the post-genomic era , 2000, Nature.
[75] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[76] C. Ouzounis,et al. Recent developments and future directions in computational genomics , 2000, FEBS letters.
[77] 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.
[78] Monica Riley,et al. Genes and proteins of Escherichia coli K-12 , 1998, Nucleic Acids Res..