Protein structure comparison by alignment of distance matrices.

By Liisa Holm, Christopher Sander. 1993

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Citations in the corpus

ECOD: An Evolutionary Classification of Protein Domains (2014, methodology): “In order to extend distant evolutionary relationships beyond the SCOP superfamily level in ECOD, we apply state of the art homology-inference algorithms both developed in our group [19,20] as well as by others [21,22], manually analyze and verify the suggested homologous links, and incorporate findi”
TM-align: a protein structure alignment algorithm based on the TM-score (2005, neutral): “Since DALI only reports those alignments of signiﬁcant Z -score and 17 086/39 800 pairs have DALI outputs, we take averages for all four methods over these 17 086 structural pairs in the lower part of Table 1.”
3D structures of membrane proteins from genomic sequencing (2012, positive): “Thepre-dicted structures of ﬁve of the proteins had similar folds to other known3Dmembraneproteinstructures(Figure2C)despitenegli-gible sequence similarity, a recurring theme seen in structural genomics and earlier work (Holm and Sander, 1993; Murzin, 1993).”
The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, methodology): “To achieve this, the Euclidean distance from the mean dm,ij dij is weighted with an exponential term analogous to the Holm/Sander approach (36).”
Mh1 domain of Smad is a degraded homing endonuclease. (2001, methodology): “Superposition was performed using InsightII package (MSI Inc) according to the DALI alignment.(37,38) A total of 152 backbone atoms of 19 residues from the two molecules superimpose with RMSD of 1.”
HorA web server to infer homology between proteins using sequence and structural similarity (2009, background): “Agreement a measures to what extent the alignments generated by different programs [DALI (30), TM-align (31) and FAST (24)] agree with one another.”
Flexible structure alignment by chaining aligned fragment pairs allowing twists (2003, methodology): “, 1996) and compared its performance with three rigid alignment programs, DALI (Holm and Sander, 1993), VAST (Madej et al.”
Emergence of Protein Fold Families through Rational Design (2006, background): “Proteins from distinct fold families, with little sequence similarity, but similar structures, constitute families of analogs (also known as superfold families) [12,19,20].”
mTM-align: a server for fast protein structure database search and multiple protein structure alignment (2018, methodology): “Many tools have been developed and the most commonly used include TM-align (5), Dali (6) and CE (7).”
3DCoffee: combining protein sequences and structures within multiple sequence alignments. (2004, methodology): “DALI produces alignments of comparable accuracy, computed by considering the local comparison of the distance maps associated with the considered structures.(28) Most of these methods make it possible to use structures for aligning sequences that are less than 30% identical.”
A historical review of recurrence plots (2008, unknown): “ the similarity matrix was re-invented by several scientiﬁc disciplines around the change from the 1970s to 1980s, and therefore different terms for the same technique, like dot plot [4], contact map [5,17], similarity matrix [22,24] or distance matrix [49] emerged. In the ﬁeld of chaos theory it fo”