ArticleProceedings of the National Academy of Sciences of the United States of America2005
Evolutionary profiles from the QR factorization of multiple sequence alignments.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Exploring the role of receptor flexibility in structure-based drug discovery.Biophysical chemistry · 2014Review
- Article
- Quantifying intramolecular binding in multivalent interactions: a structure-based synergistic study on Grb2-Sos1 complex.PLoS computational biology · 2011Article
- Recognition of the regulatory nascent chain TnaC by the ribosome.Structure (London, England : 1993) · 2010Article
- Exit strategies for charged tRNA from GluRS.Journal of molecular biology · 2010Article
- Classification and energetics of the base-phosphate interactions in RNA.Nucleic acids research · 2009Article
- Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4.BMC evolutionary biology · 2009Article
- Dynamical networks in tRNA:protein complexes.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Frequency and isostericity of RNA base pairs.Nucleic acids research · 2009Article
- An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.Journal of computer-aided molecular design · 2008Article
- Dynamics of Recognition between tRNA and elongation factor Tu.Journal of molecular biology · 2008Article
- Emergence of the universal genetic code imprinted in an RNA record.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- MultiSeq: unifying sequence and structure data for evolutionary analysis.BMC bioinformatics · 2006Article
- The evolutionary history of Cys-tRNACys formation.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Structural elements in IGP synthase exclude water to optimize ammonia transfer.Biophysical journal · 2005Article
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3 authors.
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Abstract
We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS.
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