Mining metagenomic data for novel domains: BACON, a new carbohydrate‐binding module

[1]  J. Skolnick,et al.  Monte-Carlo Simulation , 2022 .

[2]  L. Holm,et al.  The Pfam protein families database , 2011, Nucleic Acids Res..

[3]  P. Auvinen,et al.  Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein , 2009, Proceedings of the National Academy of Sciences.

[4]  J. Thornton,et al.  Missing in action: enzyme functional annotations in biological databases. , 2009, Nature chemical biology.

[5]  W. Coyle,et al.  The microbiome and obesity: Is obesity linked to our gut flora? , 2009, Current gastroenterology reports.

[6]  M. Levitt Nature of the protein universe , 2009, Proceedings of the National Academy of Sciences.

[7]  J.-X. Feng,et al.  Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens , 2009, Journal of applied microbiology.

[8]  L. Comstock Importance of glycans to the host-bacteroides mutualism in the mammalian intestine. , 2009, Cell host & microbe.

[9]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[10]  Joel Dudley,et al.  MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences , 2008, Briefings Bioinform..

[11]  U. Stenzel,et al.  PatMaN: rapid alignment of short sequences to large databases , 2008, Bioinform..

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

[13]  Robert D. Finn,et al.  Pfam 10 years on: 10 000 families and still growing , 2008, Briefings Bioinform..

[14]  D. Rigden The histidine phosphatase superfamily: structure and function. , 2008, The Biochemical journal.

[15]  Robert D. Finn,et al.  The Pfam protein families database , 2007, Nucleic Acids Res..

[16]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[17]  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[18]  Benjamin J. Raphael,et al.  The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families , 2007, PLoS biology.

[19]  E. Mardis,et al.  An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.

[20]  Narmada Thanki,et al.  CDD: a conserved domain database for interactive domain family analysis , 2006, Nucleic Acids Res..

[21]  Michael Y. Galperin,et al.  Genome‐based identification and characterization of a putative mucin‐binding protein from the surface of Streptococcus pneumoniae , 2006, Proteins.

[22]  K. Timmis,et al.  Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. , 2005, Environmental microbiology.

[23]  Ting Chen,et al.  Selecting additional tag SNPs for tolerating missing data in genotyping , 2005, BMC Bioinformatics.

[24]  F. Bäckhed,et al.  Obesity alters gut microbial ecology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

[26]  J. Walter,et al.  Construction, Analysis, and β-Glucanase Screening of a Bacterial Artificial Chromosome Library from the Large-Bowel Microbiota of Mice , 2005, Applied and Environmental Microbiology.

[27]  F. Bäckhed,et al.  Host-Bacterial Mutualism in the Human Intestine , 2005, Science.

[28]  Benjamin P. Westover,et al.  Glycan Foraging in Vivo by an Intestine-Adapted Bacterial Symbiont , 2005, Science.

[29]  W. D. de Vos,et al.  Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. , 2004, International journal of systematic and evolutionary microbiology.

[30]  Michael Y. Galperin,et al.  The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules. , 2004, Trends in biochemical sciences.

[31]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[32]  Manuel Middendorf,et al.  Discriminative topological features reveal biological network mechanisms , 2004, BMC Bioinformatics.

[33]  A. Krogh,et al.  Prediction of lipoprotein signal peptides in Gram‐negative bacteria , 2003, Protein science : a publication of the Protein Society.

[34]  J. James,et al.  A Novel Domain in AMP-Activated Protein Kinase Causes Glycogen Storage Bodies Similar to Those Seen in Hereditary Cardiac Arrhythmias , 2003, Current Biology.

[35]  Lynn K. Carmichael,et al.  A Genomic View of the Human-Bacteroides thetaiotaomicron Symbiosis , 2003, Science.

[36]  Gail J. Bartlett,et al.  Analysis of catalytic residues in enzyme active sites. , 2002, Journal of molecular biology.

[37]  Shandar Ahmad,et al.  Innovations: the gas is greener. , 2002, Environmental health perspectives.

[38]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

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

[40]  P. Wang,et al.  An intestinal mucin is the target substrate for a baculovirus enhancin. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[41]  C Kooperberg,et al.  Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.

[42]  A. Corfield,et al.  The roles of enteric bacterial sialidase, sialateO-acetyl esterase and glycosulfatase in the degradation of human colonic mucin , 1993, Glycoconjugate Journal.

[43]  B Henrissat,et al.  A classification of glycosyl hydrolases based on amino acid sequence similarities. , 1991, The Biochemical journal.

[44]  C. Peters,et al.  Phylogenetic conservation of arylsulfatases. cDNA cloning and expression of human arylsulfatase B. , 1990, The Journal of biological chemistry.

[45]  S. Barondes,et al.  Cell surface location of discoidin, a developmentally regulated carbohydrate-binding protein from Dictyostelium discoideum. , 1975, Experimental cell research.

[46]  S. Barondes,et al.  Discoidin, a developmentally regulated carbohydrate-binding protein from Dictyostelium discoideum. Purification and characterization. , 1974, Biochemistry.

[47]  D. Baker,et al.  Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins , 1999, Proteins.

[48]  E. Bloemena,et al.  Sulfomucins in the human body. , 1998, Biological chemistry.

[49]  D. Fischer,et al.  Bioinformatics Applications Note Structure Prediction Meta Server , 2022 .