makeAlignedSuperStructure: Create Protein Assembly Information

Description Usage Arguments Value Note Examples

View source: R/makeAlignedSuperStructure.R

Description

Reads the information in the PDB files to build the quaternary structure.

Usage

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makeAlignedSuperStructure(PDB_location, Assembly_location)

Arguments

PDB_location

A string pointing to the location of the *.pdb file. The pdb file provides uniprot and structural information for each residue.

Assembly_location

A string pointing to the lcoation of the *.pdb1 file. The pdb1 file provides the positional information of all the residues in the structure when they are in the asembly.

Value

aligned_structure

The aligned structure. For each residue, you get the XYZ coordinate as well as other structural information. The absPos column in the aligned_structure variable matches the absPos column in the raw_structure and is used for debugging purposes. The canonical_pos column represents the residue number in the fasta sequence for the subunit with the specified uniprot id. The canonical_pos column can repeat. For instance, if there are two proteins, A and B, in the assembly, both proteins may have residue #5 in them. The absPos column will not repeat.

aa_table

A table showing the pairwise alignment between the residue sequence as specified by the pdb file and the residue sequence specified by the fasta sequence in the uniprot database. This table is mainly used for debugging.

raw_structure

The raw structure as read in from the *.pdb1 file after some cleaning. For instance, row's with NA for uniprot values are dropped. Further, only the carbon-alpha rows are kept.

Note

This method reads fasta information from www.uniprot.org. Thus an internet connection is required in order to execute properly.

This functionality is still in beta. The user is encouraged to check the alignment created by the method.

Examples

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#read the pdb file
pdb.location <- "https://files.rcsb.org/view/1A6Z.pdb"
assembly.location <- "https://files.rcsb.org/download/1A6Z.pdb1"


(alignment.results <- makeAlignedSuperStructure(pdb.location, assembly.location))

QuartPAC documentation built on Nov. 1, 2018, 4:27 a.m.