Computational protocol: Computational analysis of prolyl hydroxylase domain-containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans

Similar protocols

Protocol publication

[…] The PHD2 (isoform 1) and LIMD1 sequences (accession code: Q9GZT9 and Q9UGP4, respectively) were downloaded from Uniprot. Homologous sequences for both proteins were retrieved and selected from OMA Browser using standard parameters and visualized using Jalview. Multiple sequence alignments (MSA) for PHD2 and LIMD1 were built with Clustal Omega and used as input for conservation analysis with Consurf. A conservation score was calculated with the Scorecons server, using default parameters. Secondary structure prediction was performed with PSIPRED, while prediction of intrinsic disorder was performed using C-Spritz. MobiDB was used to compare disorder predictions obtained for the human PHD2 with PHD orthologs. The presence of linear motifs was investigated using the ELM server. The sequence logo for LIMD1 was built with WebLogo and interacting residues were predicted with Anchor. […]

Pipeline specifications

Software tools Jalview, Clustal Omega, ConSurf, PSIPRED, WebLogo
Application Genome data visualization
Organisms Homo sapiens
Diseases Neoplasms, Polycythemia
Chemicals Oxygen