Computational protocol: Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens

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Protocol publication

[…] We used the Dali Database for structure comparisons (downloaded in January 2009), and the Human Protein Reference Database (HPRD), HHPID and PIG for protein interactions (downloaded February, July and June 2009, respectively) [-,,]. The literature sources and various databases used each have their own system of identifiers. PDB codes obtained from Dali were mapped to their corresponding taxonomy and Uniprot accessions using data from the SIFTS initiative [,,]. Other identifier mappings were carried out using DAVID Gene ID Conversion or Uniprot ID mapping [-]. Network diagrams were created in Cytoscape []. Images of protein structures were created in MacPyMol []. […]

Pipeline specifications

Software tools DALI, DAVID
Databases HPRD
Application Protein structure analysis
Organisms Human immunodeficiency virus 1, Homo sapiens, Human immunodeficiency virus 2
Diseases HIV Infections