Difference between revisions of "Foldseek"

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(Created page with "Category:SoftwareCategory:BiologyCategory:Bioinformatics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|foldseek}} |{{#vardefine:url|https://github.com/steineg...")
 
 
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
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|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 
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|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
 
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
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* HPC_{{uc:{{#var:app}}}}_DB - database directory
  
 
<!--Configuration-->
 
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<!--Run-->
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
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Examples illustrating use of $HPC_FOLDSEEK_DB:
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foldseek easy-search $HPC_FOLDSEEK_DIR/foldseek/example/d1asha_ $HPC_FOLDSEEK_DB/PDB/pdb aln2.m8 tmp
  
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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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==
  
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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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:
  
WRITE_CITATION_HERE
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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 website  

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)