Using Dali for Protein Structure Comparison.

By Liisa Holm. 2020

481 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH (2022, methodology): “GDT_TS scores were calculated using the AS2TS server 57 and possible structural similarities were assessed using Dali 58 .”
Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine (2022, methodology): “A pdb 627 file was generated and used for structural homology searches using the Dali Server(Holm, 2020).”
Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex (2022, methodology): “Interface area was calculated with PISA (Krissinel and Henrick, 2007) and coordinate superposition with COOT or DALI (Holm, 2020).”
Fast and accurate protein structure search with Foldseek (2022, methodology): “Most structural aligners, such as the popular TM-align, Dali and CE 11,13,14 , solve the alignment optimization problem by iterative or stochastic optimization.”
DeepTracer ID: De Novo Protein Identification from Cryo-EM Maps (2022, methodology): “Therefore, after scoring all AlphaFold2 predictions, we use the DaliLite v5 27 to perform an all-to-all analysis on the top hits.”
Rethinking Protein Drug Design with Highly Accurate Structure Prediction of Anti-CRISPR Proteins (2021, methodology): “The Dali Z-score is the sum of the equivalent residue-wise intermolecular distances among two proteins, and does not have a ﬁxed upper bound [40].”
Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein (2020, methodology): “Sequence alignment of ORF7a and ORF8 and secondary structure annotations were guided by Define Secondary Structure of Proteins through the DALI server (27) and manually adjusted based on visual inspection of the structures.”
B-Cell Epitope Mapping of TprC and TprD Variants of Treponema pallidum Subspecies Informs Vaccine Development for Human Treponematoses (2022, methodology): “DALI software (39) and PDB analyses to identify structurally similar porins (Table S1) showed that the highest-scoring structures did not contain the exact number of b-strands predicted by AlphaFold2 for TprC and TprD2 b-barrels, but slightly higher or slightly lower, but well within the models of i”