Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Lateral tunnel automatic detection

AC Adrien H. Cerdan
LP Laurie Peverini
JC Jean-Pierre Changeux
PC Pierre-Jean Corringer
MC Marco Cecchini
ask Ask a question
Favorite

We used the MOLEonline webserver (https://mole.upol.cz) (26) to detect lateral tunnels within PDB structures of various conformational states of the receptor. We used default parameters but the following: Probe radius set to 40, Interior Threshold set to 1.4, Bottleneck Radius set to 1.4, Bottleneck Tolerance set to 0, and Max Tunnel Similarity set to 0.15.

Copyright and License information:  ©2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).
This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A