User guide
The Initialisation Panel (see Figure 1) is located on the Home page, enabling the user to upload the structure to MOLEonline.
-
PDBID - access the structure directly from the Protein Data Bank in Europe using the CoordinateServer service. It is possible to import only one structure at a time. Optionally, an Assembly ID can be used to upload the targeted part of the structure.
-
File - upload structure from computer files. The molecular structures can be uploaded in PDB or mmCIF formats. ZIP and GZIP archives are supported up to the maximum file size of 100 MB. For example, you can prepare structure only with chain A with removed ligand molecule.
-
Last session - access the previous session. Each session has a random ID assigned to ensure private access.
Figure 1. Initialisation panel on the Home page
The interface is structured with the following components. On the left, you can find a panel where switching between the Compute and Channels panels is possible.
Figure 2 – MOLEonline Computation detail webpage for cytochrome P450 3A4 (PDB ID 1TQN)
Users can switch the submission settings to Pore mode and Channels mode in the Compute panel.
-
Pore mode focuses on detecting transmembrane pores using membrane positioning data from the OPM database or the MEMEMBED program. Parameters include the option to calculate pores only within the transmembrane region and settings tailored for β-barrel structures.
-
Channels mode enables the identification of channels and other pore types. Users can define start and end points manually or use automatic definitions. Adjustable parameters include probe radius, surface coverage, bottleneck tolerance and more.
For a comprehensive description of all parameters and options, please refer to the Documentation.
Firstly, you can choose from the automatic starting points. Loading a structure will trigger the automatic detection procedure. Once the structure is loaded, you can click on one of these options on the Compute panel on the left side.
- CSA – residues from the Catalytic Site Atlas
- Origins – either CSA Origins (green balls) or Computed origins in each cavity (blue balls)
- Cofactor starting points
Or use your own starting point (see Figure 3):
- Exact residue, atom or point – you can choose it directly in the structure by clicking on the position
- Choose residue in the Protein Sequence
- Using PatternQuery language
- Choose the tetrahedron on the structure's surface by Ctrl + left mouse if you intend to compute pores or paths
The Submit button is in the Compute panel's bottom left corner.
Figure 3 – Interactive selection of start and end points via residues or XYZ coordinates. The endpoint can be selected as a facet on the surface with a Ctrl + left mouse click.
Parameters from previous calculations can be easily reloaded. Once the channels are calculated, the submission parameters for the macromolecular structure can be exported in JSON format (see Figure 4). These parameters can be reloaded in future sessions using the Load params button, enabling a new calculation to determine the channels.
The Load params is in the Compute panel's bottom right corner.
Figure 4 – Example of settings used for submission of calculation of channels at result webpage for PDB ID 1TQN.
Interactive channel visualisation runs in Mol* Viewer. Here, you can visualise various graphical elements, such as loaded structures or any cavities, tunnels, and pores that have been found. Additional graphical elements include the molecular surface, along with tunnel start points and tunnel exit points. Mol* allows using several representations, such as sticks, cartoons, lines, etc., to visualise the structure and the computed channels or pores.
Channels can be coloured according to their physicochemical properties (see Figure 5). We significantly enhance our understanding of molecular interactions by visualising these channels based on attributes such as charge or hydrophobicity.
Figure 5 – The channel is displayed with colour coding based on hydrophobicity on the results webpage for PDB ID 1K4C.
Visualizing 2D diagrams of secondary structures within domains is possible using 2DProts (see Figure 6). Offered diagrams visualise the relative distance between single secondary structure elements and the position of amino acids that comprise each element in the sequence of the domain. The 2D diagram contains two types of symbols that represent secondary structures:
- Arrow: represents a strand
- Bar: represents a helix
Users can view the diagram by clicking on 2DProts at the bottom left of the visualisation window. The diagram can be exported by clicking on Download SVG.
Figure 6 – Visualization of 2D diagram computed by 2DProts on the results webpage for PDB ID 1K4C.
Users can download the report of the computed channels or pores by clicking the Download button in several formats in the upper left corner of the visualisation window. You can choose from Molecule (cif), PyMol, VMD, PDB, Chimera, JSON, PDF Report or as a complete zip file containing all computed data (structures, channel profiles, and physicochemical properties)
Additionally, individual channel profiles can be downloaded by clicking the Export button next to the profile and selecting either PNG or SVG format.