Bug reporting

If you encounter an error or have an idea for an improvement, please send us an email: [email protected] or open a GitHub issue. Thank you!

Limitations

MOLEonline was designed to analyze static structures identified through X-ray, NMR or cryo-EM experiments, so it cannot directly provide any information about the breathing motions of detected channels. In addition, ligand passage along the channel/pore may cause significant digestive motions, which should be considered during the interpretation of results. The physicochemical properties are calculated only from amino acids lining the channel/pore, and the reported values do not cover nonstandard amino acids, cofactors and nucleic acids. MOLEonline cannot detect pores whose diameter is smaller or the same as the length due to the MOLE algorithm for cavities identification. Nevertheless, MOLEonline is able to calculate channels in structures containing up to ∼60k residues in a reasonable time.

Browser compatibility

OS	Version	Chrome	Firefox	Edge	Safari
Linux	Fedora 37			X	X
Windows	Windows 10	X	X	X
MacOS	Big Sur 11.6			X

References

[Cid1992] (Cid, H., Bunster, M., Canales, M. and Gazitúa, F. (1992) Hydrophobicity and structural classes in proteins. Protein Eng. Des. Sel., 5, 373–375. https://doi.org/10.1093/protein/5.5.373

[Jones1992] Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) The Rapid Generation of Mutation Data Matrices from Protein Sequences. Bioinformatics, 8, 275–282. https://doi.org/10.1093/bioinformatics/8.3.275

[Kyte1982] (Kyte, J. and Doolittle, R.F. (1982) A Simple Method for Displaying the Hydropathic Character of a Protein. J. Mol. Biol., 157, 105–132. https://doi.org/10.1016/0022-2836(82)90515-0

[Lomize2006]Lomize, M.A., Lomize, A.L., Pogozheva, I.D. and Mosberg, H.I. (2006) OPM: Orientations of Proteins in Membranes Database. Bioinformatics, 22, 623–625. https://doi.org/10.1093/bioinformatics/btk023

[Nugent2013] Nugent, T. and Jones, D.T. (2013), Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics, 14, 276. https://doi.org/10.1186/1471-2105-14-276

[Zimmerman1968] Zimmerman, J.M., Eliezer, N. and Simha, R. (1968) The Characterization of Amino Acid Sequences in Proteins by Statistical Methods. J. Theor. Biol., 21, 170–201. https://doi.org/10.1016/0022-5193(68)90069-6