COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance.

By Ruslan I. Sadreyev, Nick V. Grishin. 2003

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In Molecular Biology

Citations in the corpus

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields (2014, methodology): “Quite a few PSSM-based profile comparison methods for homology detection have been developed, including [11, 18-23].”
The HHpred interactive server for protein homology detection and structure prediction (2005, methodology): “In a recent study (28), in which we bench-marked HHsearch, the method for HMM–HMM comparison employed by our server, together with PSI-BLAST, HMMER, PROF_SIM and COMPASS (3,6,7,29), HHsearch was found to possesses the highest sensitivity and alignment accuracy.”
Progress and challenges in protein structure prediction. (2008, methodology): “There are alternatives in calculating the PPA scores [20].”
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).”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, methodology): “Sequence±structure matches are established by aligning the target sequence pro®le against the template pro®les, using local dynamic programming in the SALIGN module and an assessment of statistical signi®cance similar to that of PSIBLAST (22) and COMPASS (23).”
Comparative Protein Structure Modeling Using Modeller (2006, methodology): “The simultaneous use of several templates can minimize this kind of error (Srinivasan and Blundell, 1993; Sanchez and Sali, 1997a; Sanchez and Sali, 1997b).”
Analysis of CASP8 targets, predictions and assessment methods (2009, background): “Nevertheless, nine consensus match residues in the COMPASS alignment map to structurally equivalent positions validating the OB-fold hit and suggesting a possible evolutionary relationship with Nucleic acid-binding domains.”
Alignment of protein sequences by their profiles (2004, methodology): “First, the dot product between two distributions Pi and Qi at profile positions i and j, respectively: Si,j 1 = a Pi,a Qj,a ( 6) Second, the correlation coefficient between two distributions Pi and Qj: Si,j 2 = a Pi,a Qj,a a Pi,a Pi,a Qj,a Qj,a ( 7) Third, the Euclidean distance between two distribu”
PhyLAT: a phylogenetic local alignment tool (2012, methodology): “In Sadreyev and Grishin (2003), a rescaling technique was explored to use a standard score distribution to estimate statistical significance of profile alignments of new profiles.”
PISCES: recent improvements to a PDB sequence culling server (2005, methodology): “These purposes include statistical analysis of certain structural features, such as side-chain rotamer distributions (2), benchmarking sequence alignment and structure prediction methods (3), and analysis of a set of proteins, such as those with a certain function (e.”
Improving protein fold recognition by random forest (2014, methodology): “For profile-profile alignment features, five profile-profile alignment tools CLUSTALW, COACH of LOBSTER [42], COMPASS [43], HHSearch [44] and PRC (Profile Compiled, http://supfam.org/ PRC) were used to align target and template profiles to obtain profile-profile alignment scores.”
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison (2010, methodology): “At the same time COMA, COMPASS and PSI-BLAST all show relative performance qualitatively similar to that of the global mode.”
PROMALS: towards accurate multiple sequence alignments of distantly related proteins (2007, methodology): “J.Pei and N.V.Grishin alignment methods such as PSI-BLAST (Altschul et al., 1997) and COMPASS (Sadreyev and Grishin, 2003).”