Finding weak similarities between proteins by sequence profile comparison.

By Anna R. Panchenko. 2003

60 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Comparative Protein Structure Modeling Using Modeller (2006, methodology): “…of variants of profile-profile alignment methods that differ in the scoring functions they use (Pietrokovski, 1996; Rychlewski et al., 1998; Yona and Levitt, 2002; Panchenko, 2003; Sadreyev and Grishin, 2003; von Ohsen et al., 2003; Edgar, 2004; Marti-Renom et al., 2004; Zhou and Zhou, 2005).”
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre (2008, unknown): “The 10 FR-systems used in the Phyre ensemble are methods 8, 9, 10, 11, 12, 13, 21, 22, 25, and 31.”
Comparative Protein Structure Modeling Using MODELLER (2016, background): “…number of variants of proﬁle-proﬁle alignment methods that differ in the scoring functions they use (Pietrokovski, 1996; Rychlewski et al., 1998; Yona and Levitt, 2002; Panchenko, 2003; Sadreyev and Grishin, 2003; von Ohsen et al., 2003; Edgar, 2004; Marti-Renom et al., 2004; Zhou and Zhou, 2005).”
Alignment of protein sequences by their profiles (2004, methodology): “Several methods that align protein sequences by comparing their profiles have been described (Pietrokovski 1996; Jaroszewski et al. 2000; Yona and Levitt 2002; Edgar and Sjolander 2003a; Panchenko 2003; Sadreyev and Grishin 2003).”
Protein homology detection by HMM?CHMM comparison (2005, unknown): “tors are 3.3 (COMPASS), 6.0 (PROF_SIM), 7.3 (HMMER), 9.4 (PSI-BLAST), and 63 (BLAST).10 In several recent benchmark studies, column scores for profile‐profile alignment were compared for their ability to produce alignments similar to structure-based alignments (Mittelman et al., 2003; Panchenko, 20”
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains (2016, background): “Even more sensitive tools carry out profile-profile searches, which extract familywide information for both query and target((4-6)).”
Comparative Protein Structure Modeling Using MODELLER (2016, 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).”
Comparative Protein Structure Modeling Using MODELLER (2007, background): “It is imperative to calculate an accurate alignment between the target-template pair, as comparative modeling can almost never recover from an alignment error (Sanchez and Sali, 1997a).”