Load Fasta

The fasta node automatically infers which type of data is contained in which file and generates the correct type of reference to be used with other nodes.

Input: file name

Output: fasta file in one of the formats (protein, nucleic acid, aligned protein, aligned nucleic acid, multi protein, multi nucleic acid).

Load GenBank

Converts a GenBank file into a fasta file. This node exports the gene sequence from the GenBank file to a gene fasta file while preserving the annotations in the file’s selections.

Input: GenBank file

Output: fasta file

Load PDB

Load a protein structure in PDB format.

Input: file name

Output: PDB file

Load SDF

Load a molecular structure in SDF format.

Input: file name

Output: SDF file

Smiles to structure

This node converts a SMILES (Simplified molecular-input line-entry system) string, given as text, into an SDF format structure. The SDF file format stores three-dimensional structural data of molecules like drugs or metabolites. (see Additional file formats).

The optimize option determines if xyna.bio should optimize the three-dimensional geometry of the molecule using molecular mechanics. This can be useful to obtain a more accurate three-dimensional structure of the molecule.

Input: SMILES string in text form

Output: SDF file

Add SDF to PDB

Adds a SDF structure to a PDB structure. Returns a PDB file with the added SDF ligand.
Note: this does not perform any docking, the coordinates of both the protein and ligand are conserved as is. To position the ligand along the protein structure, please perform docking beforehand.

Input: PDB file, SDF file

Output: PDB file

Merge Fasta

Merges two protein fasta sequences into one multi fasta file.

Input: fasta file

Output: fasta file

Extract Selection from Structure

Gets a substructure of a given PDB file based upon the name of a previously defined selection. Returns all amino acids within the selection range as a new PDB structure. Does not return water molecules or other types of atoms present in the PDB file.

Input: PDB file

Output: PDB file of substructure

Extract Selection from Fasta

Extracts a subsequence from a fasta sequence based upon a selection name of a previously defined selection (see Annotation Nodes).

Input: fasta file

Output: fasta file of subsequence