id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6346	Speed up AlphaFold search	Tom Goddard	Goddard	"Currently the ""alphafold match"" command currently takes about 20 seconds, using BLAT (not BLAST) on the AlphaFold database of 1 million sequences.  It hangs ChimeraX while waiting.  EBI plans to eventually extend to 100 million sequences.  In July of 2021 the database was introduced with 350K sequences and increased to 1 million in January 2022, so it has increased by 650K in 6 months.  Search is probably 3 times slower now.

Investigate other search programs that might be faster, such as HMMER or MMSEQS2.

Ideally we'd want search to run under 10 seconds.
"	enhancement	assigned	moderate		Structure Prediction								all	ChimeraX