Difference between revisions of "Foldseek"
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional 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 | |
|}} | |}} | ||
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{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} 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) | |
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|}} | |}} | ||
Latest revision as of 18:07, 25 August 2024
Description
Foldseek enables fast and sensitive comparisons of large protein structure sets.
Environment Modules
Run module spider foldseek to find out what environment modules are available for this application.
System Variables
- HPC_FOLDSEEK_DIR - installation directory
- HPC_FOLDSEEK_BIN - executable directory
- HPC_FOLDSEEK_DB - database directory
Additional 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)