template_ligand_search.py Command Help
Command: $SCHRODINGER/run -FROM psp template_ligand_search.py
usage: $SCHRODINGER/run -FROM psp template_ligand_search.py
Script to search the biolip database for homologous receptors.
Performs a BLAST search of the receptor sequence against entries in BioLip,
followed by a series of optional filters, returning a list of hits ranked
primarily by the BLAST E-value, along with relevant information.
Structures of hits are downloaded and aligned to the input receptor, if
one was provided. Using the '-skip_download' option skips the downloading.
In addition to filtering hits by sequence or structure properties, it is
possible to add an additional ligand similarity filter, by providing a
ligand structure (or SMILES string) and the '-min_tanimoto' option.
Example invocations:
* Search for ligand-bound homologs of a receptor provided as a structure
$SCHRODINGER/run -FROM psp template_ligand_search.py -rec rec.mae
* Start the search from a PDB ID
$SCHRODINGER/run -FROM psp template_ligand_search.py -pdb_id 3eml
* Search for homologs of a chain of the receptor
$SCHRODINGER/run -FROM psp template_ligand_search.py -pdb_id 3sn6 -chain_id R
* Return top 10 hits
$SCHRODINGER/run -FROM psp template_ligand_search.py -rec rec.mae -num_output_hits 10
* Do not download hit structures, produce only .csv file summary of hits
$SCHRODINGER/run -FROM psp template_ligand_search.py -rec rec.mae -skip_download
* Return hits with receptor sequence identity > 30%
$SCHRODINGER/run -FROM psp template_ligand_search.py -rec rec.mae -min_identity 30.0
* Return hits with ligand Tanimoto similarity > 0.3 to the ligand in lig.mae
$SCHRODINGER/run -FROM psp template_ligand_search.py -rec rec.mae -lig lig.mae -min_tanimoto 0.3
* Exclude hits with specified UniProt IDs
$SCHRODINGER/run -FROM psp template_ligand_search.py -rec rec.mae -exclude_uniprot UNP101010 UNP101011
* Return only hits with specified UniProt IDs
$SCHRODINGER/run -FROM psp template_ligand_search.py -rec rec.mae -filter_by_uniprot UNP101010
options:
-h, --help show this help message and exit
-jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
Optional name for template search job.
Receptor Options:
-rec RECEPTOR, -receptor RECEPTOR
Input structure of the query receptor.
-fasta FASTA File containing the receptor sequence to query, in
FASTA format.
-pdb_id PDB_ID PDB ID of the receptor to query. To specify a
particular chain, use the -chain_id option
-chain_id CHAIN_ID Chain to extract from the query receptor structure.
This option is required when the input structure or
input PDB ID have more than one chain.
Ligand Options:
-lig LIG Ligand structure to use when filtering hits.
-lig_smiles LIG_SMILES
Ligand SMILES string to use when filtering hits.
-lig_asl LIG_ASL ASL to specify ligand molecule in the receptor
structure.
-min_tanimoto MIN_TANIMOTO
Minimum Tanimoto similarity value of ligands to input
ligand. Hits with a similarity value below this
threshold will be ignored.
-max_tanimoto MAX_TANIMOTO
Highest Tanimoto similarity value of ligands to input
ligand. Hits with a similarity value above this
threshold will be ignored.
Sequence Search Options:
-max_blast_homologs MAX_BLAST_HOMOLOGS
Maximum number of hits to return from BLAST search.
(default: 500).
-min_identity MIN_IDENTITY
Minimum sequence identity (%) to query sequence
required for BLAST hits. Hits with sequence identity
below this threshold will be ignored. (default: 25.0)
-max_identity MAX_IDENTITY
Highest sequence identity (%) to query sequence
required for BLAST hits. Hits with sequence identity
above this threshold will be ignored. (default: None)
-min_similarity MIN_SIMILARITY
Minimum sequence similarity (%) to query sequence
required for BLAST hits. Hits with sequence similarity
below this threshold will be ignored.
-max_similarity MAX_SIMILARITY
Highest sequence similarity (%) to query sequence
required for BLAST hits. Hits with sequence similarity
above this threshold will be ignored.
-max_evalue MAX_EVALUE
Highest E-value allowed for BLAST hits. Hits with an
E-value above this threshold will be ignored.
(default: 10.0).
ID Filtering Options:
-exclude_uniprot UNIPROT_EXCLUDE_SET [UNIPROT_EXCLUDE_SET ...]
Uniprot accession numbers to exclude from the results.
For example, '-exclude_uniprot A2BC19 P12345' excludes
all hits matching any of the two accession numbers.
Unless a specific isoform is provided (e.g. P12345-1),
all isoforms matching the parent accession will be
excluded.
-exclude_uniprot_file UNIPROT_EXCLUDE_SET
File listing uniprot accession numbers to exclude from
the results. Should contain one accession number per
line. See help string of -exclude_uniprot for more
details.
-filter_by_uniprot UNIPROT_FILTER_SET [UNIPROT_FILTER_SET ...]
Uniprot accession numbers to select from the results.
For example, '-filter_by_uniprot A2BC19 P12345'
returns only hits matching any of the two accession
numbers. Unless a specific isoform is provided (e.g.
P12345-1), all isoforms matching the parent accession
will be selected.
-filter_by_uniprot_file UNIPROT_FILTER_SET
File listing uniprot accession numbers to select from
the results. Should contain one accession number per
line. See help string of -filter_by_uniprot for more
details.
-exclude_taxid TAXID_EXCLUDE_SET [TAXID_EXCLUDE_SET ...]
NCBI taxonomy identifiers to exclude from the results.
For example, '-exclude_taxid 9606' excludes all human
hits.
-exclude_taxid_file TAXID_EXCLUDE_SET
File listing NCBI taxonomy identifiers to exclude from
the results. Should contain one identifier per line.
See help string of -exclude_taxid for more details.
-filter_by_taxid TAXID_FILTER_SET [TAXID_FILTER_SET ...]
NCBI taxonomy identifiers to select from the results.
For example, '-filter_by_taxid 9606' returns only
human hits.
-filter_by_taxid_file TAXID_FILTER_SET
File listing NCBI taxonomy identifiers to select from
the results. Should contain one identifier per line.
See help string of -filter_by_taxid for more details.
wwPDB Search Filters:
-from_date FROM_DATE Earliest date (in ISO format, YYYY-MM-DD) to include
hits. Date is compared to the original structure
initial release date as recorded in the wwPDB. For
example, -from_date 2024-01-01 will only produce hits
released on and after Jan 1, 2024.
-until_date UNTIL_DATE
Latest date (in ISO format, YYYY-MM-DD) to include
hits. Date is compared to the original structure
initial release date as recorded in the wwPDB. For
example, -until_date 2023-12-31 will only produce hits
released until Dec 31, 2023.
-max_resolution MAX_RESOLUTION
Maximum structure resolution value to consider when
selecting hits. Structures with resolution above this
threshold will be ignored. Note that this option does
not affect NMR structures as these do not have a
defined resolution.
-include_nmr Include NMR structures in the results.
Output Options:
-num_output_hits NUM_OUTPUT_HITS
Number of final hits to write to output .csv file.
Note that this is an upper limit - the actual search
might return less hits.
-skip_download Skip downloading annotated hit structures.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-D, -DEBUG Show details of Job Control operation.
-NOJOBID Run the job directly, without Job Control layer.
Standard Options:
-NOLAUNCH Set up subjob inputs, but don't run the jobs.