id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15825	Add a PDB and AlphaFold database sequence search using RCSB mmseqs2	Tom Goddard	Tom Goddard	"It might be useful to add a PDB and AlphaFold database sequence search that uses RCSB web services.  Currently we offer BLAST sequence search in ChimeraX which is slower especially for large databases.  The RCSB explains on their web pages they use the fast and modern mmseqs2 instead of BLAST for searches from their web page.

My main interest in this is that I wanted to allow my new structure comparison tools (backbone traces, sequence plots, ligand aggregation, umap clustering) to work on collections of hundreds of structures from methods other than foldseek.  I considered making these capabilities work with BLAST, but it seems that mmseqs2 searches have mostly supplanted BLAST, giving similar sensitivity with much higher speed for handling the large databases (AlphaFold).  Since mmseqs2 was developed by the same group that make Foldseek (Steinegger lab), its web service works almost exactly the same and the returned results are very similar.  So the current foldseek code and result display can almost work with an mmseqs2 server."	enhancement	closed	moderate		Sequence		fixed						all	ChimeraX