Structural alignment: Difference between revisions

Revision as of 19:48, 7 May 2023

Revision as of 19:49, 11 May 2023

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Mammoth makes no attempt to re-iterate the initial alignment or extend the high quality sub-subset. Therefore, the seed alignment it displays can't be fairly compared to DALI or TM align as it was formed simply as a heuristic to prune the search space. (It can be used if one wants an alignment based solely on local structure-motif similarity agnostic of long range rigid body atomic alignment.) Because of that same parsimony, it is well over ten times faster than DALI, CE and TM-align.<ref name="foldclass">{{cite journal

|title=Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments

|authorsauthor1=Pin-Hao Chi, |author2=Bin Pang, |author3=Dmitry Korkin, |author4=Chi-Ren Shyu

|journal=Bioinformatics

|volume=25

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|pmid= 15598351

|title=SCOPmap: Automated assignment of protein structures to evolutionary superfamilies

|authorsauthor1=Sara Cheek, |author2=Yuan Qi, |author3=Sri Krishna, |author4=Lisa N Kinch, and |author5=Nick V Grishin

|page= 197

|pmc= 544345

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<ref name="fssa">{{cite journal

|title=FSSA: a novel method for identifying functional signatures from structural alignments

|authorsauthor1=Kai Wang, |author2=Ram Samudrala

|journal=Bioinformatics

|year=2005

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It has been particularly successful at analyzing "decoy" structures from ab initio structure prediction.<ref name="casp11">{{cite journal

|authorsvauthors=Kryshtafovych A, Monastyrskyy B, Fidelis K.

|title=CASP11 statistics and the prediction center evaluation system. \

|journal=Proteins

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<ref name="Malmstrom">{{cite journal

|title=Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology

| authorsauthor1=Lars Malmström Michael Riffle, |author2=Charlie EM Strauss, |author3=Dylan Chivian, |author4=Trisha N Davis, |author5=Richard Bonneau, |author6=David Baker

|year=2007

|journal=PLOS Biol