Table 3.
List of software and methods for tunnel detection and transportation phenomena observation.
| Software or method | Applicability |
Remarks | |
|---|---|---|---|
| System | Functionality | ||
| AQUA-DUCT [79], [80] | Mus musculus epoxide hydrolase | water molecule tracking | can be used also for cavity and hot-spot detection Standalone: link |
| d-amino-acid oxidase [111] | tunnel and gating residue detection | ||
| Pyrococcus furiosus phosphoglucose isomerase [93] | water molecule tracking and occupancy analysis in the internal cavity | ||
| Claudin-2 ion channel [112] | ion transportation pathways identification | ||
| Solvent flux method[107] | Candida antarctica lipase B | identification of water access pathway; hot-spot identification | based on an artificial gradient. Code not available. |
| Streamline tracing [105] | photosystem II | fibre tracing; tunnel detection; gating residue (access control points) identification | visual analysis only; code available on request |
| squalene–hopene cyclase [106] | changes in water flow after introducing amino acid substitution | ||
| trj_cavity[108]* | Der p 2 protein; TM pore; pullulanase | generating the trajectory of discovered cavities, quantification of time-dependent cavity volume, solvent presence inside a particular cavity; tunnel detection | implemented in GROMACS: link |
| polydicyclopentadiene [114]; herkinorin [115]; glycidoxypropyltrimethoxy silane [116]; mammalian translocator membrane protein [117]; human G-protein coupled receptors [118]; amyloid fibrils [119]; sperm whale myoglobin [120]; 07A metalloprotease [121]; human erythrocyte anion exchanger 1 (Band 3 protein) [122]; amorphous silica [123]; full-length TLR4 dimer [124]; profilin [125]; human serum albumin [126]; laccase [127]; dengue capsid protein (C protein) [128]; horseradish peroxidase; lactoperoxidase [129]; OmpC–MlaA complex [130], [131], [132]; MATE transporter [133] | cavity analysis | ||
| cholesteryl ester transfer protein [134]; acyl carrier proteins [135] | time-dependent cavity analysis | ||
| mouse myoglobin [109] | analysis of the movement of ligands, movements within the cavities and tunnels of proteins | ||
| Visual Abstractions of Solvent Pathlines[104] | TEM β‐lactamase[136] | identification of the role of water in gating loop flexibility | visual analysis only; code not available |
| Watergate [113] | haloalkane dehalogenase mutants | visualisation of water molecule trajectories | visual analysis only; code available on request |
*For trj_cavity software only recent applications are presented (2017–2019). Information about currently unavailable software is in italics.