Comparison of sequence profiles. Strategies for structural predictions using sequence information

By Leszek Rychlewski, Weizhong Li, Lukasz Jaroszewski, Adam Godzik. 2008

493 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields (2014, methodology): “Many different methods can be used to measure node and edge similarity of two MRFs, just like many different scoring functions can be used to measure the similarity of two PSSMs or HMMs.”
Protein homology detection by HMM?CHMM comparison (2005, background): “A number of structure prediction servers exist that rely on profile– profile comparison (Rychlewski et al., 2000; Ginalskiet al., 2003; Tang et al., 2003; von Öhsenet al., 2003; Tomii and Akiyama, 2004).”
Ultrafast clustering algorithms for metagenomic sequence analysis (2012, methodology): “In GOS, these steps include (i) calculation of all-against-all similarities using BLAST; (ii) construction of core sequence clusters, which are dense sub-graphs in the whole graph where the vertices are sequences and the edges are defined by a set of very strong similarities cutoffs; (iii) calculati”
Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding (2011, background): “Most work in this area has focused on developing more sensitive pairwise comparisons between the query and target sequences, including sequence-sequence local alignments (BLAST [1], Smith-Waterman [2]); profile-sequence (PSI-BLAST [3]) and HMM-sequence comparisons (HMMER [4]); and, most recently, pr”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, methodology): “In the core set merging step, we constructed an FFAS (Fold and Function Assignment System) profile [39] for each core set using the longest sequence in the core set as query.”
Using multiple templates to improve quality of homology models in automated homology modeling (2008, methodology): “In a recent study (Wallner and Elofsson 2006), we showed that three methods, Nest (Petrey et al. 2003), Modeller (Sali and Blundell 1993), and SegMod (Levitt 1992), all perform quite well for single-template homology modeling, while several other methods frequently failed to produce…”
MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information (2008, methodology): “31–34 For example, in LiveBench-8,31 all top four servers (BASD/MASP/ MBAS, SFST/STMP, FFAS03, and ORF2/ORFS) are based on the sequence profile–profile alignment.”
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins (2003, methodology): “In many cases HMM or Profile methods (40) will provide complementary or more sensitive detection with respect to regular expressions and we plan to provide both.”
Finding weak similarities between proteins by sequence profile comparison. (2003, background): “The sensitivity of the pro®le, or maximum radius of detection of remote family members, has been shown to depend on the diversity of the sequences included in the multiple alignment/pro®le (16,40,41).”
Pcons5: combining consensus, structural evaluation and fold recognition scores (2005, methodology): “In total 10,974 protein models for these eleven servers were used: PDB–BLAST [23], FFAS [23], Sam-T99 [16], mGenTHREADER [14], INBGU [7], three FUGUE servers [25], 3D-PSSM [18], Orfeus [11] and Superfamily [13].”
Alignment of protein sequences by their profiles (2004, methodology): “Similarly, the FFAS program was developed to align two sequence profiles with each other (Jaroszewski et al. 2000; Rychlewski et al. 2000 ).”
Protein structure prediction and analysis using the Robetta server (2004, methodology): “Ginzu is a hierarchical screening procedure that ﬁrst uses BLAST, PSI-BLAST (10), FFAS03 (11,12) and 3D-Jury (13,14) to detect regions in the query sequence that are homologous to experimentally determined structures, and then proceeds with multiple sequence alignment (MSA) based methods to predict ”
COMPASS server for homology detection: improved statistical accuracy, speed and functionality (2009, background): “An alternative empirical approach of comparing real unrelated proteins (3,6,7, 10 ,11) requires an additional calibration on a database of diverse protein representatives, and can generate only a limited random sample of similarity scores, which hinders the precise analytical fitting of the empirica”
GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome (2015, methodology): “LOMETS is a multi-threading approach consisting of nine complementary threading algorithms from FFAS (sequence profile-profile match) (Rychlewski et al., 2000), HHsearch (hidden Markov model to hidden Markov model alignment) (Soding, 2005), MUSTER (multiple resource profile-profile alignment) (Wu an”