3D-footprint April 2022 version

Hi,

3D-footprint, our database for the structural analysis of protein-DNA complexes, has been up and running since 2010 (see https://doi.org/10.1093/nar/gkp781). Due to a hardware failure it had been last updated in 2021. Finally we found the time to bring the system up to speed again, now in a Debian environment, and will be releasing new protein-DNA complexes from the PDB quarterly. We will also add the new content to footprintDB.

 

What's new?

• codebase is pretty much the same
• the URL is now https://floresta.eead.csic.es/3dfootprint
• the updated downloadables can be found at https://floresta.eead.csic.es/3dfootprint/download.html
• the original ineractive tool to analyze your own protein-DNA complexes has now been replaced with a Docker container at https://hub.docker.com/r/eeadcsiccompbio/dnaprot
  

 That's all for today,

Bruno

Consultas GraphQL al Protein Data Bank

Hola, 

durante el mantenimiento anual de footprintDB he descubierto que el Protein Data Bank ha cerrado su interfaz de web servicios (WS) https://www.rcsb.org/pages/webservices/rest-fetch .  Leyendo en https://data.rcsb.org/index.html#data-api veo que ahora se pueden hacer consultas REST o GraphQL, y opté por la segunda por aprender un poco.

Hay documentación en https://data.rcsb.org/migration-guide.html#legacy-fetch-api para migrar las consultas WS antiguas a GraphQL. Las nuevas consultas tienen este aspecto:

query={
 entry(entry_id:"9ANT"{
  polymer_entities{
   rcsb_polymer_entity{
    pdbx_description
   }
   rcsb_entity_source_organism{
    scientific_name
   }
   rcsb_polymer_entity_container_identifiers{
    entry_id
    auth_asym_ids
    reference_sequence_identifiers{
     database_accession,
     database_name
    }
   }
  }
  struct{
   title
  }
  rcsb_primary_citation{
   pdbx_database_id_PubMed
  }
 }
}

Y se pueden convertir a una URL como https://data.rcsb.org/graphql?query={entry(entry_id:%229ANT%22){polymer_entities{rcsb_polymer_entity{pdbx_description}rcsb_entity_source_organism{scientific_name},rcsb_polymer_entity_container_identifiers{entry_id,auth_asym_ids,reference_sequence_identifiers{database_accession,database_name}}}struct{title}rcsb_primary_citation{pdbx_database_id_PubMed}}}

 

Si haces click verás que en Chrome o Firefox no obtienes el resultado esperado, con un error:

Invalid character found in the request target. The valid characters are defined in RFC 7230 and RFC 3986

Creo que se debe a un problema del servidor Tomcat del PDB. Sin embargo, sí funciona con wget y así obtienes la salida JSON que puedes procesar con tu lenguaje favorito:

wget 'https://data.rcsb.org/graphql?query={entry(entry_id:%229ANT%22){polymer_entities{rcsb_polymer_entity{pdbx_description}rcsb_entity_source_organism{scientific_name},rcsb_polymer_entity_container_identifiers{entry_id,auth_asym_ids,reference_sequence_identifiers{database_accession,database_name}}}struct{title}rcsb_primary_citation{pdbx_database_id_PubMed}}}' -O-

Hasta pronto,

Bruno