foldseek¶
Description¶
Foldseek enables fast and sensitive comparisons of large structure sets.
Environment Modules¶
Run module spider foldseek to find out what environment modules are available for this application.
Environment Variables¶
- HPC_FOLDSEEK_DIR - installation directory
- HPC_FOLDSEEK_BIN - executable directory
- HPC_FOLDSEEK_DB - database directory
Additional Usage Information¶
Examples illustrating use of $HPC_FOLDSEEK_DB:
foldseek easy-search $HPC_FOLDSEEK_DIR/foldseek/example/d1asha_ $HPC_FOLDSEEK_DB/PDB/pdb aln2.m8 tmp
foldseek easy-multimersearch $HPC_FOLDSEEK_DIR/foldseek/example/1tim.pdb.gz $HPC_FOLDSEEK_DB/PDB/pdb result tmp
Citation¶
If you publish research that uses foldseek you have to cite it as follows:
van Kempen, M., Kim, S.S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C.L.M., Söding, J., and Steinegger, M. Fast and accurate protein structure search with Foldseek. Nature Biotechnology, doi:10.1038/s41587-023-01773-0 (2023)
Categories¶
bioinformatics