Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

By Rachel Kolodny, Patrice Koehl, Michael Levitt. Journal of Molecular Biology, 2005

316 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/752b9dee597661ffe76956706227f25560bbc56c

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Citations in the corpus

Advances and pitfalls of protein structural alignment. (2009, background): “Þ (to be minimized) Similarity index (SI) [11] Norm 1 (cid:4) 1 þ N e ð 1 þ rmsd = 1 : 5 Þð 1 þ min ð N A ; N B ÞÞ Match index (MI) [11] Norm max u 2 PUU ð A Þ ; 2 PUU ð B Þ 0 : 5 Dali’s empirical Z -score.”
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures (2007, methodology): “As Kolodny et al. [29] highlight, not all structural comparison methods are as good at scoring their alignments as they are at producing them.”
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately (2010, methodology): “The gold-standard answer includes neighbors found by a best-of-six structural aligner (using SSAP (26), STRUCTAL, DALI (27), LSQMAN (28), CE, and SSM); this expensive computation was done previously (10).”
Matt: Local Flexibility Aids Protein Multiple Structure Alignment (2008, methodology): “More sophisticated geometric scoring measures have also been suggested, some to collapse the bi-criteria optimization problem into a single score to be optimized [28], such as the Structal score [1], others to incorporate more environmental information into the similarity measure, such as secondary ”
ASH structure alignment package: Sensitivity and selectivity in domain classification (2007, methodology): “With regard to the SAS score, STRUCTAL does the best, in agreement with the findings of Kolodny, et al. [3], followed by GASH; however, when we consider the NER score, GASH performs the best, followed by DaliLite.”
TM-align: a protein structure alignment algorithm based on the TM-score (2005, unknown): “In fact, a variety of different evaluation methods have been considered in the literature (22).”
A novel method to compare protein structures using local descriptors (2011, background): “Even in the category of the most straightforward approaches which focus on finding the largest possible sets of superimposable amino-acids, treating structures as rigid entities and preserving the order of aligned residues, there is no definitive “best of all” method [1].”
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee (2006, methodology): “In 3D-Coffee, the principle is the same except that the library’s pairwise alignments are derived from structural superpositions using methods like Sap (13), Lsqman (14) or possibly any alternative structure alignment package [for a review see (15)].”
CATH: an expanded resource to predict protein function through structure and sequence (2016, background): “Structal (20), TM-Align (21)) did not significantly improve performance.”
DALI and the persistence of protein shape (2019, background): “Because each program optimizes its alignments with respect to the program's native scoring function, this type of evaluation 49 – 52 informs on the similarity of the program's native score to the evaluator's canonical score.”
PDBe: Protein Data Bank in Europe (2010, result): “sourceforge.net/). Studies have shown that the algorithm is particularly efficient ( 46 ), compared with similar”