MOLEonline Updates
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Input
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mmCIF parsing
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Added PatternQuery language support (ignore residues, start points).
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Automatic starting points from cavities in 3D structure - Origin points
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Transmembrane Pore mode
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Parameters of calculation
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Selection of end points (It is possible to compute tunnels to only 1 user specified exit)
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New weight functions for computing tunnels (added Length, Voronoi scale weight functions)
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Computation of "User Pores" now works for any cavity, not just the "surface".
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Selection of end points with Ctrl+left click
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Pore mode
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Enhancement of transmembrane pore calculations with use of OPM database or MEMEMBED program
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Vizualization of membrane region
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Visualization
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LiteMol instead of Jmol
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Layered Channel profile with physicochemical properties
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Multiple layers can be selected/deselected to show average properties and list of residues only around important area of the channel.
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Connectivity to ChannelsDB
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New properties
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Free Radius for channels (Free Radius is the distance to the closest backbone or HET atom)
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BRadius for channels (BRadius is the Radius + RMSF (from Bfactors) to estimate local flexibility)
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Lipophilicity (logP and logD@pH 7.4 scales of channel-lining residues)
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Water solubility (logS-like scale of channel-lining residues)
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Export of results
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Ability to export residues surrounding a cavity or channel
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CSV output of properties along the individual channels
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Export current computation settings in XML
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Rich JSON output for programmatic analysis
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Export of channel profile in PNG or SVG format
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Output to PyMOL, VMD, and Chimera.
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Export of results for individual channels to PDF report or within ZIP archive
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User contributions to ChannelsDB annotations
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better macromolecular surface representation (probe radius in MOLE 2 vs. convex hull in MOLE 1.4)
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no need to determine the number of channels prior calculation
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quicker calculation due to the division of the internal space within the macromolecule to separate sub-cavities
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better removal of duplicate channels (surface cover radius parameter, similar channels with RMSD < 0.5 A are reported only once in shorter variant)
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automatic selection of the starting points based on detected cavities
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better visualization of the starting points and their optimized position
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experimental feature - calculation of physicochemical properties of the residues lining the channel