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MOLEonline web interface provides direct access to MOLE functionality and enables online and easy-to-use detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The web-based application enables two calculation modes: i) one is dedicated to analysing channels, while ii) the other is specifically designed for transmembrane pores. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB 2.0, OPM, UniProt, PDBsum, and PDBe-KB) to help set up and analyse acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels and information about their numerous physicochemical features.
- User guide step-by-step guide to using the MOLEonline web application
- Documentation information about the features and functionality of the web application
- Method describes the channel detection algorithm used in MOLE
- FAQ Frequently Asked Questions to address common queries
- About contains contact information, limitations and references related to the wiki
Channel calculation
- Tunnels from the starting point to the surface or any other endpoint
- Automatic transmembrane Pores
- Help form with integrated submission for easier support
Input
- PDB and mmCIF files
- PDBe integration
- PatternQuery language support (ignore residues, start points)
Parameters of calculation
- Automatic starting points from cavities in 3D structure - Origin points
- Selection of starting/end points in sequence, residue selection, or XYZ point
- Selection of endpoints (It is possible to compute tunnels to only one user-specified exit) with Ctrl+left click
- Several weight functions for computing tunnels (Length, Voronoi scale weight functions)
- Computation of "User Pores" now works for any cavity, not just the "surface"
Pore mode
- Enhancement of transmembrane pore calculations with the use of the OPM database or MEMEMBED program
- Visualization of membrane region
Visualization
- Mol* Viewer for visualization of structure
- Colouring of channels based on physicochemical properties
- Layered Channel profile with physicochemical properties and residue lists
- Multiple layers can be selected/deselected to show average properties and a list of residues only around important areas of the channel
- Connectivity to ChannelsDB
- 2D diagrams of secondary structures using 2DProts
Properties of channels
- Geometrical properties
- Length, Radius, Free Radius and BRadius
- Physicochemical properties
- Charge, Mutability, Polarity, Hydropathy, Hydrophobicity, Lipophilicity, Water solubility
Export of results
- Output of visualisation of channel analysis in mmCIF format
- Export parameter for calculation of channel - JSON
- Properties of channels - CSV, XML, JSON
- Channel profile in PNG or SVG format
- Output visualization to PyMOL, VMD, and Chimera
- PDF report or within ZIP archive
Previous versions
- MOLEonline (2018) - Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vařeková R, Koča J, Otyepka M: MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Research, 46(W1), W368–W373, 2018. (DOI)
- MOLEonline 2.0 - Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu CM, Svobodová Vařekova R, Koča J, Otyepka M: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res., 40(W1), W222-W227, 2012. (DOI)