Flexible structure alignment by chaining aligned fragment pairs allowing twists

By Yuzhen Ye, Adam Godzik. 2003

637 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Toward the estimation of the absolute quality of individual protein structure models (2010, methodology): “As in the work of Robinson-Rechavi and Godzik, proteins were shortened according to a structural alignment (FATCAT w/o flexibility, (Ye and Godzik, 2003)) in order to get homologous protein pairs of similar size.”
ProDCoNN: Protein design using a convolutional neural network (2019, background): “The amino acids shown below the true label row are alternative amino acids at the corresponding position based on the sequences which are similar (P-value = 0, twist = 0) with 1a3nA calculated by FATCAT.(65) An orange background indicates exactly correct prediction, and a blue background indicates t”
Matt: Local Flexibility Aids Protein Multiple Structure Alignment (2008, methodology): “While flexibility has been introduced into the study of protein folding in the context of docking [31,32], particularly for the modeling of ligand binding [33], and more recently in decoy construction for ab initio folding algorithms [34,35], it has only recently been incorporated into general-purpo”
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures (2019, methodology): “…contacts atlas (18), PDBe-KB and PDBe-PISA (19) as well as a range of resources for structure comparison and searches such as DALI (20), FATCAT (21), TOPMATCH (22) and PDBe-Fold (19) allowing users to compare and search for structural similarities using different structure comparison…”
Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism (2018, positive): “We identified representative protein domains for this set of genes using a structure-based clustering algorithm 32 .”
The RCSB Protein Data Bank: new resources for research and education (2012, methodology): “Pairwise alignments of the domains are performed with the jFatCat version (24) of FatCat (22).”
The RCSB Protein Data Bank: redesigned web site and web services (2010, methodology): “This tool utilizes new Java implementations of the CE (13) and FATCAT (14) structure-alignment algorithms and provides references to external structure alignment servers.”
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity (2014, background): “Flexible alignment methods overgo this limitation by either allowing twists between rigidly aligned fragments (Menke et al., 2008; Ye and Godzik, 2003) or by only maximizing local (in terms of Euclidean distance) similarities (Godzik and Skolnick, 1994; Wohlers et al.”
FATCAT: a web server for flexible structure comparison and structure similarity searching (2004, methodology): “The FATCAT algorithm has been implemented in a fast and efﬁcient computer program written in C ++ and systematically tested on large alignment benchmarks (12).”
MMDB and VAST+: tracking structural similarities between macromolecular complexes (2013, methodology): “The Protein Data Bank, for example, reports structure neighbors from a subset of representatives computed with the jFATCAT algorithm (10) and points to a handful of external resources that provide structural classifications and structure comparisons: SCOP (11), CATH (12), VAST (8), FATCAT (13), DALI”
BioJava: an open-source framework for bioinformatics in 2012 (2012, methodology): “It contains Java ports of the FATCAT algorithm (Ye and Godzik, 2003) for flexible and rigid body alignment, a version of the standard Combinatorial Extension (CE) algorithm (Shindyalov and Bourne, 1998) as well as a new version of CE that can detect circular permutations in proteins (Bliven and Prli”
A novel method to compare protein structures using local descriptors (2011, methodology): “To specifically address structural shifts and distortions, some methods search for “ hinges ” between superimposable rigid parts (FATCAT [22], FlexProt [23], ProtDeform [24], FlexSnap [25]).”
Pre-calculated protein structure alignments at the RCSB PDB website (2010, neutral): “There is a difference in how initial D w n l the consequence that different regions of a protein structures undergo different geometric transformations f r .”