Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.

By Jong H. Park, Kevin J. Karplus, Christian Barrett, Richard Hughey, David Haussler, Tim J. P. Hubbard, Cyrus Chothia. 1998

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Citations in the corpus

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields (2014, methodology): “Early methods such as [24] usually conduct straightforward comparison of feature vectors, but are not very sensitive [25].”
Finding weak similarities between proteins by sequence profile comparison. (2003, background): “With the rapid increase in the number of protein sequences and thoroughly characterized protein families, it has been shown that statistical properties of protein families are very important in most cases in establishing the correct evolutionary connections between sequences in the sequence space (8”
RSDB: representative protein sequence databases have high information content (2000, background): “It has been shown that iterative multiple sequence search algorithms can be at least two times more sensitive with a test set of distant homologues [PDB40D: 40% sequence identity or less to each other, Park et al. (1998)].”
Comparative Protein Structure Modeling Using MODELLER (2016, background): “The proﬁle-sequence meth-ods are more sensitive in detecting related structures in the twilight zone than the pair-wise sequence-based methods; they detect approximately twice the number of homologs under 40% sequence identity (Park et al., 1998; Lindahl and Elofsson, 2000; Sauder et al., 2000).”
Improvement of the GenTHREADER Method for Genomic Fold Recognition (2003, methodology): “, 1997), SAM-T98 (Park et al., 1999) and FFAS (Rychlewski et al.”
Comparative Protein Structure Modeling Using MODELLER (2016, background): “…used to model the calcium-bound state of the target, it is likely that the model will be incorrect irrespective of the target-template Modeling Structure from Sequence 5.6.25 Current Protocols in Bioinformatics Supplement 54 similarity or accuracy of the template structure (Pawlowski et al., 1996).”
CDD: a database of conserved domain alignments with links to domain three-dimensional structure (2002, background): “Protein sequence comparison, as a tool to investigate patterns of conservation and divergence in molecular evolution, is more powerful when sequences are compared to models of protein families instead of other single sequences (1).”
Alignment of protein sequences by their profiles (2004, methodology): “A particularly successful method in this class is implemented in the SAM package (Hughey and Krogh 1996) that outperforms other sequence-based methods for fold recognition (Karplus et al. 1998; Park et al. 1998; Madera and Gough 2002).”
Enhanced genome annotation using structural profiles in the program 3D-PSSM. (2000, methodology): “In trials based on recognising remote homologues identi®ed on the basis of similar 3D structure, PSI-Blast and hidden Markov models gave comparable results, which were far superior to single-sequence search methods (Park et al., 1998).”
On Prediction Using Variable Order Markov Models (2004, methodology): “Of all models, the HMM model is perhaps the most popular and successful model for protein classification to-date (Park et al., 1998).”
Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.011544. (2003, unknown): “It has been noted previously that profile methods are able to retrieve remote homologs and that they are approximately three times more efficient than pair-wise comparisons (Park et al., 1998).”
Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “The proﬁle-sequence methods are more sensitive in detecting related structures in the twilight zone than the pairwise sequence-based methods; they detect approximately twice the number of homologs under 40% sequence identity (Park et al., 1998; Lindahl and Elofsson, 2000; Sauder et al., 2000).”