Functionalities regarding protein Structures

This workflow offers several functionalities to explore the consequence of protein mutations. It reports features that overlap the mutations, or that are in close physical proximity.

The features reported include protein domains, variants, helices, ligand binding residues, catalytic sites, transmembrane domains, InterPro domains, and known somatic mutations in different types of cancer. This information is extracted from resources such as UniProt, COSMIC, InterPro and Appris. It can also identify mutations affecting the interfaces of protein complexes.

This workflow makes use of PDB files to calculate residues in close proximity. This information is used to find features close to the mutations, at a distance of 5 angstroms, or mutations in residues close to residues in a complex partner, at a distance of up to 8 angstroms.

PDBs are extracted from Interactome3d, which organized thousands of PDBs, for both experimental structures and structure models, of individual proteins and protein complexes.

Pairwise (Smith-Waterman) alignment is used to fix all inconsistencies between protein sequences in PDBs, Uniprot and Ensembl Protein ID.

Reference:

Vazquez M, Valencia A, Pons T. (2015) Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. Bioinformatics (2015); 31(14):2397-2399 (doi: 10.1093/bioinformatics/btv142)

Tasks

The annotation tasks take either genomic mutations or mutated isoforms. Mutated isoforms must be in reference to Ensembl Protein IDs (e.g. ENSP00000449454:E433D). When inputing genomic mutations, the consequence of this mutations in terms of mutated isoforms is computed automatically. Genomic mutations can be reported in Chromosome:Position:AlternativeAllele format (e.g. 1:19949995:T) or in VCF format. Normaly genomic mutations are given always with respect to the Watson or forward strand. This is the default. Sometimes, however, mutations are given with respect to the strand that encodes de gene; If this is the case, specify watson to be false. The version of the methods using mutated isoforms as input have the _mi_ term in their name. The organism input is used to specify the version of the genome and gene set to use, leave Hsa for the most recent Homo sapiens data, or Hsa/may2009 for the latest gene set of hg18. The date codes correspond the Ensembl archives, which are used to download and process all the information consistently for each version.

When PDBs are required, the PDB code or a URL can be specified using the pdb parameter. Alternatively, the content of a PDB file can be provided using the pdbfile parameter.

The result of these tasks are reported in TSV tables. These tables often encode complex relationships. For instance a genomic mutation might have as consequence several mutated isoforms, with each protein mutation overlapping different domains or features. This multiplicity is encoded in the TSV in a standard way: using tabs to separate fields, vertical bars (|) to separate diferent values for each field, and semicolons (;) to further separate multiple options for each result.

The main tasks are: annotate, annotate_neighbours, and interfaces. Or alternatively for mutated isoforms: annotate_mi, annotate_mi_neighbours, and mi_interfaces.

All the workflow tasks can be executed from the web interface, programatically, through the REST interface using wget or curl, or using the rbbt command. See the rbbt documentation for more information.

annotate

Annotates genomic mutations based on the protein features that are overlapping amino-acid changes

annotate_neighbours

Annotates genomic mutations based on the protein features that are in close physical proximity to amino-acid changes

At a distance of 5 angstroms

interfaces

Find variants that affect residues in protein-protein interaction surfaces

Residues at a distance of 8 angstroms of a residue from an interaction partner

annotate_mi

Annotates mutated isoforms based on the protein features that are overlapping amino-acid changes

annotate_mi_neighbours

Annotates mutated isoforms based on the protein features that are in close physical proximity to amino-acid changes

At a distance of 5 angstroms

mi_interfaces

Find mutated_isoforms with affected residues in protein-protein interaction sufaces

Residues at a distance of 8 angstroms of a residue from an interaction partner

mi_neighbours

Finds residues physical proximity to amino-acid changes in mutated isoforms

At a distance of 5 angstroms

neighbour_map

For a given PDB, find all pairs of residues in a PDB that fall within a given 'distance' of each other. It uses PDBs from Interactome3d for individual proteins.

neighbours_in_pdb

Use a pdb to find the residues neighbouring, in three dimensional space, a particular residue in a given sequence.

pdb_alignment_map

Find the correspondence between sequence positions in a PDB and in a given sequence. PDB positions are reported as chain:position.

pdb_chain_position_in_sequence

Translate the positions of amino-acids in a particular chain of the provided PDB into positions inside a given sequence.

sequence_position_in_pdb

Translate the positions inside a given amino-acid sequence to positions in the sequence of a PDB by aligning them

wizard

Run a list of variants through all the analysis and produce a combined report. This analysis is limited to 1000 variants (use the other more granular methods otherwise). Variants can be expressed as genomic mutations or protein mutations. When protein mutations are used, the name of the protein can be Ensembl Protein ID or any other protein or gene identifier, including gene symbols (e.g. KRAS:G12V)

scores

Score a list of variants based on the report generated by the wizard. The limitation to 1000 variants still holds.

score_summary

Produce a small table summarizing the mutation scores and a few of the features