ArticleNucleic acids research1997
Extracting protein alignment models from the sequence database.
Article in Nucleic acids research, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- RNA-hydrolyzing activity of metallo-β-lactamase IMP-1.PloS one · 2020Article
- Molecular modeling and QM/MM calculation clarify the catalytic mechanism of β-lactamase N1.Journal of molecular modeling · 2019Article
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- Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20.Metallomics : integrated biometal science · 2016Review
- The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase.The Journal of biological chemistry · 2016Article
- Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.PLoS computational biology · 2016Article
- Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing.Human immunology · 2015Article
- Linkage of catalysis and 5' end recognition in ribonuclease RNase J.Nucleic acids research · 2015Article
- Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.BMC bioinformatics · 2012Article
- The CphAII protein from Aquifex aeolicus exhibits a metal-dependent phosphodiesterase activity.Extremophiles : life under extreme conditions · 2012Article
- Analysis of the functional contributions of Asn233 in metallo-β-lactamase IMP-1.Antimicrobial agents and chemotherapy · 2011Article
- Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains.Structure (London, England : 1993) · 2011Article
- Article
- Giardia duodenalis 14-3-3 protein is polyglycylated by a tubulin tyrosine ligase-like member and deglycylated by two metallocarboxypeptidases.The Journal of biological chemistry · 2011Article
- Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.Statistical applications in genetics and molecular biology · 2011Article
- Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.Bioinformatics (Oxford, England) · 2009Article
- The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches.Journal of molecular biology · 2009Article
- The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops.BMC structural biology · 2009Article
- Discovering sequence motifs with arbitrary insertions and deletions.PLoS computational biology · 2008Article
- Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis.Journal of bacteriology · 2006Article
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Authors and funding
4 authors.
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Abstract
Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called Probe fully automates this process of model construction starting from a single sequence. Central to this program is a powerful new method to locate and align only those, often subtly, conserved patterns essential to the family as a whole. When applied to randomly chosen proteins, Probe found on average about four times as many relationships as a pairwise search and yielded many new discoveries. These include: an obscure subfamily of globins in the roundworm Caenorhabditis elegans ; two new superfamilies of metallohydrolases; a lipoyl/biotin swinging arm domain in bacterial membrane fusion proteins; and a DH domain in the yeast Bud3 and Fus2 proteins. By identifying distant relationships and merging families into superfamilies in this way, this analysis further confirms the notion that proteins evolved from relatively few ancient sequences. Moreover, this method automatically generates models of these ancient conserved regions for rapid and sensitive screening of sequences.
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