Author Search Demo¶

pdbj

Example query for human protein-serine/threonine kinases using SIFTS data retrieved with PDBj Mine 2 webservices.

References¶

The “Structure Integration with Function, Taxonomy and Sequence” is the authoritative source of up-to-date residue-level annotation of structures in the PDB with data available in UniProt, IntEnz, CATH, SCOP, GO, InterPro,Pfam and PubMed. SIFTS

Data are provided through: Mine 2 SQL

Queries can be designed with the interactive PDBj Mine 2 query service

Imports¶

In [2]:

from pyspark import SparkConf, SparkContext
from mmtfPyspark.webfilters import PdbjMineSearch
from mmtfPyspark.mappers import StructureToPolymerChains
from mmtfPyspark.io import mmtfReader

Configure Spark Context¶

In [3]:

conf = SparkConf().setMaster("local[*]") \
                  .setAppName("KinaseDemo")
sc = SparkContext(conf = conf)

Query for human protein-serine/threonine kinases using SIFTS data¶

In [4]:

sql = "SELECT t.pdbid, t.chain FROM sifts.pdb_chain_taxonomy AS t  "\
            + "JOIN sifts.pdb_chain_enzyme AS e ON (t.pdbid = e.pdbid AND t.chain = e.chain) "\
            + "WHERE t.scientific_name = 'Homo sapiens' AND e.ec_number = '2.7.11.1'"

Read PDB and filter by author¶

In [6]:

path = "../../resources/mmtf_reduced_sample/"

pdb = mmtfReader.read_sequence_file(path, sc) \
                .flatMap(StructureToPolymerChains()) \
                .filter(PdbjMineSearch(sql))

print(f"Number of entries matching query: {pdb.count()}")

Number of entries matching query: 2722

Terminate Spark Context¶

In [7]:

sc.stop()

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