Dali: a network tool for protein structure comparison.

By Liisa Holm, Christopher Sander. 1995

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Citations in the corpus

TM-align: a protein structure alignment algorithm based on the TM-score (2005, neutral): “TM-align is also faster than two other often-used algorithms, CE (17) and DALI (38), and yet provides structure alignments of higher TM-score (which is not surprising since maximization of the TMscore is the goal of the TM-align objective function).”
3D structures of membrane proteins from genomic sequencing (2012, neutral): “…predicted adiponectin receptor 3D structures are surprisingly similar ( (cid:1) 4.5 A˚ C a -rmsd over 204 residues) to the bacteriorhodopsin crystal structure (PDB: 3hao), with highly signiﬁcant Dali (Holm and Sander, 1995) Z scores between 7 and 13, despite negligible sequence identity (8”
Comparison of performance in successive CASP experiments (2001, methodology): “For CASPs 1 and 2, lists of the potential template structures to each target were generated using DALI.(3) For CASPs 3 and 4, these lists were generated using PROSUP.”
DALI and the persistence of protein shape (2019, methodology): “The wider use of automated structure comparison programs was propelled by their availability as network services.(7,8) The automated methods allowed all-against-all structure comparison and clustering of all known structures, that is, the mapping of fold space.”
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors (2013, methodology): “The DALI algorithm and server (13) is used to compare structures, and if the z-score from the DALI comparison to that of an existing member of a clan is >6.”
Dali server: conservation mapping in 3D (2010, background): “The Dali server has evolved to cope with the growth of the PDB, which is now a hundred times bigger than when the server started (8).”
How significant is a protein structure similarity with TM-score = 0.5? (2010, methodology): “The purpose of the gapless alignment is to generate a random structure background, because a structural alignment, produced by tools such as Dali (Holm and Sander, 1995) and TM-align (Zhang and Skolnick, 2005), usually represents an optimal match of a given pair of protein structures that is selecte”
Scoring function for automated assessment of protein structure template quality (2004, background): “ments for protein modeling quality in the literature.(1,2,15,19,20,22,23) With MAMMOTH(19) for example, Ortiz and coworkers assess structures by comparing both local and global similarities.”