molclaw-protein-sequence-retrieve

name	molclaw-protein-sequence-retrieve
description	Search the target protein sequence information from the input gene name or uniprot id.
license	MIT license
metadata	{"skill-author":"PJLab"}

Retrieve Target Protein Sequence

Note:

• Local files are not directly accessible by the server. Please upload them to the server using molclaw-file-transfer before execution.
• For PDB file inputs, it is recommended to preprocess them using molclaw-pdbfixer before execution.
• Please refer to skill molclaw-scp-server to complete tool invocation.

The description of tool retrieve_protein_sequence.

Retrieve protein sequence data for a given identifier (gene name or uniprot id) and organism.
Args:
    identifier (str): Input gene name (e.g., 'TP53') or uniprot id (e.g., 'P04637')
    organism (str): Required species name, e.g. "Homo sapiens"
Return:
    status (str): success/error
    msg (str): message
    seq_info (dict): A dict containing uniprot_id, gene_name, protein_name, organism, sequence, length

How to use tool retrieve_protein_sequence :

response = await client.session.call_tool(
    "retrieve_protein_sequence",
    arguments={
        "identifier": identifier,
        "organism": organism
    }
)
result = client.parse_result(response)
prot_sequence_info = result["seq_info"]

An example of output sequence information:

{'uniprot_id': 'O76074', 'gene_name': 'PDE5A', 'protein_name': "cGMP-specific 3',5'-cyclic phosphodiesterase", 'organism': 'Homo sapiens', 'length': 875, 'sequence': 'MERAGPSFGQQRQQQQPQQQKQQQRDQDSVEAWLDDHWDFTFSYFVRKATREMVNAWFAERVHTIPVCKEGIRGHTESCSCPLQQSPRADNSAPGTPTRKISASEFDRPLRPIVVKDSEGTVSFLSDSEKKEQMPLTPPRFDHDEGDQCSRLLELVKDISSHLDVTALCHKIFLHIHGLISADRYSLFLVCEDSSNDKFLISRLFDVAEGSTLEEVSNNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKSSDTLTREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFPWTTENTGNVNQQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQNTQMYEAVERAMAKQMVTLEVLSYHASAAEEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEKMLINGESGQAKRN', 'query_input': 'PDE5A'}