US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
By Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang. 2022
437 citations recorded by the source corpus.
Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules—proteins, RNAs and DNAs. The pipeline is built on a uniform TM-score objective function coupled with a heuristic alignment searching algorithm. Large-scale benchmarks demonstrated consistent advantages of US-align over state-of-the-art methods in pairwise and multiple structure alignments of different molecules. Detailed analyses showed that the main advantage of US-align lies in the extensive optimization of the unified objective function powered by efficient heuristic search iterations, which substantially improve the accuracy and speed of the structural alignment process. Meanwhile, the universal protocol fusing different molecular and structural types helps facilitate the heterogeneous oligomer structure comparison and template-based protein–protein and protein–RNA/DNA docking. US-align is a universal protocol for monomeric and oligomeric structural alignments of protein, RNA and DNA molecules, built on the coupling of a uniform TM-score objective function and the heuristic iterative searching algorithm.
Subfields: Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Andriy Kryshtafovych
- Torsten Schwede
- Krzysztof Fidelis
- Yang Zhang
- John Moult
- Rhiju Das
- R. Rangan
- Bohdan Monastyrskyy
Citations in the corpus
- Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “29,31 For R1138 (720 nt), d 0 = 13.59 Å and most of the residues in a visually good model like R1138TS232_4 align within this threshold in the TM-score calculation.”
- New prediction categories in CASP15 (2023, background): “This is the oligomeric Template Modeling score (TM-score) 49 for overall topology (SCORE) and the contact based QS-score 50 which is interface centric (QSCORE).”