Advances and pitfalls of protein structural alignment.

By Hitomi Hasegawa, Liisa Holm. Current Opinion in Structural Biology, 2009

404 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9fc2e3d95d44ae9b60b65edb6de4a2030015fff9

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Fast Multiple Alignment of Protein Structures Using Conformational Letter Blocks (2009, neutral): “[1, 2].”
Fast and accurate protein structure search with Foldseek (2022, background): “This illustrates that 3D aligners such as TM-align may overlook homologous structures that are not globally superposable, whereas Foldseek (as well as the two-dimensional (2D) aligner Dali) is independent of relative domain orientations and excels at detecting homologous multi-domain structures 12 .”
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity (2014, background): “Many protein structure comparison methods have been proposed and there is no consensus which one is the best (Godzik, 1996; Hasegawa and Holm, 2009), as the alignments that maximize different scoring schemes can differ considerably (Mayr et al.”
Dali server update (2016, background): “A large variety of scoring functions have been proposed (15).”
The RCSB Protein Data Bank: new resources for research and education (2012, methodology): “Sequence and structure alignments are standard methods for analyzing the evolutionary and functional relationship between proteins (18–23).”
A novel method to compare protein structures using local descriptors (2011, background): “For an alternative classification, see a recent review [26].”
Dali server: conservation mapping in 3D (2010, background): “A wide spectrum of structural alignment methods exist, which diﬀer in their treatment of structural variations, scoring functions and optimization algorithms [reviewed in (1)].”
DALI and the persistence of protein shape (2019, background): “It is important to note that the scoring function of DALI is not designed to optimize rigid-body superimposition, 26 although the program outputs a root-mean-square deviation (RMSD) and superimposed coordinates, because this is customary and, in many cases, gives an informative visualization of…”
MMDB and VAST+: tracking structural similarities between macromolecular complexes (2013, background): “In the past 25 years, a variety of methods have been developed to computationally characterize ormeasure structural similarities between macromolecules, resulting in an even larger variety of published methods, too numerous to be listed here (9).”