Alignment of protein sequences by their profiles

By Marc A. Martí-Renom, Mallur Srivatsan Madhusudhan, Andrej Sali. 2004

197 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): “The resulting profile-sequence alignments correctly align approximately 43% to 48% of residues in the 0% to 40% sequence identity range (Sauder et al., 2000; Marti-Renom et al., 2004); this number is almost twice as large as that of the pairwise sequence methods.”
Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives (2012, methodology): “SAM[31],HMMER[32] or profileprofile alignment such as FFAS03[33], profilescan[34] and HHsearch.”
Protein structure modeling with MODELLER. (2014, methodology): “Apart from model building, MODELLER can perform auxiliary tasks such as fold assignment, alignment of two protein sequences or their profiles(15), multiple alignment of protein sequences and/or structures(16,17), clustering of sequences and/or structures, and ab initio modeling of loops in protein s”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, methodology): “ModPipe uses sequence–sequence (22), sequence–profile (19,23) and profile–profile (5,24) methods for fold assignment and target–template alignment, using a promiscuous E-value threshold of 1.”
ModBase, a database of annotated comparative protein structure models and associated resources (2013, background): “Sequence–structure matches are established using a variety of fold-assignment methods, including sequence–sequence (14), profile–sequence (15,16) and profile–profile alignments (16, 17 ).”
Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “The resulting proﬁle-sequence alignments correctly align approximately 43% to 48% of residues in the 0% to 40% sequence identity range (Sauder et al., 2000; Marti-Renom et al., 2004); this number is almost twice as large as that of the pair-wise sequence methods.”
SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model (2008, methodology): “SALIGN benchmark [42] contains 200 selected pairs with an average pair sharing 20% sequence identity and 65% of structurally equivalent C a atoms superposed with an rmsd of 3.5 A˚ Reference alignment is obtained from the structural alignment obtained from the TMalign program [43] [i.e., TM overlap].”
Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments (2014, methodology): “6 [30] with templates and multiple sequence alignments taken from the SALIGN benchmark study [39, 40] (downloaded from http://salilab.”
SPARKS 2 and SP3 servers in CASP6 (2005, background): “12,14–17 Another way to detect structural similarity is via sequence-to-structure threading.”
COBALT: constraint-based alignment tool for multiple protein sequences (2007, background): “Alignment to a profile is significantly more sensitive to subtle relationships between sequences (Gribskov et al ., 1987; Marti-Renom et al ., 2004).”
Structural bioinformatics A machine learning information retrieval approach to protein fold recognition (2006, unknown): “…et al., 2003b; Sadreyev and Grishin, 2003; Edgar and Sjolander, 2003, 2004; Ohlson et al., 2004; Wallner et al., 2004; Wang and Dunbrack, 2004; Marti-Renom et al., 2004; Söding, 2005) are even more sensitive at detecting distant homologs and compatible structures, and often achieve even…”
Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences (2007, methodology): “Among the most successful approaches that use this strategy are profile alignment algorithms that use database search to find related sequences for each input sequence, construct a profile from the hits, and then align the profiles instead of the sequences, including algorithms that start from two s”