Next Article in Journal
Identification and Characterization of Process-Related Impurities of Trans-Resveratrol
Previous Article in Journal
Synthesis of 1,2,3-Triazole Derivatives and Evaluation of their Anticancer Activity
Article Menu

Article Versions

Export Article

Scientia Pharmaceutica is published by MDPI from Volume 84 Issue 3 (2016). Articles in this Issue were published by another publisher in Open Access under a CC-BY (or CC-BY-NC-ND) licence. Articles are hosted by MDPI on as a courtesy and upon agreement with Austrian Pharmaceutical Society (Österreichische Pharmazeutische Gesellschaft, ÖPhG).
Open AccessShort Communication
Sci. Pharm. 2013, 81(3), 677-682;

How to Solve the Problems of Docking into a Symmetric Binding Site: The Example of the hERG Channel

University of Vienna, Department of Medicinal Chemistry, Althanstraße 14, 1090, Vienna, Austria
Author to whom correspondence should be addressed.
Received: 1 July 2013 / Accepted: 31 July 2013 / Published: 31 July 2013
PDF [128 KB, uploaded 28 September 2016]


Many proteins, such as the hERG K+ channel or the HIV-1 protease, have a high degree of rotational symmetry. If the binding site of a ligand is composed of symmetrical subunits, the analysis of the docking poses of ligands is quite challenging. In the case of hERG, the four-fold symmetry of the entire channel is fully reflected in the binding site, which allows up to four poses with different coordinates of the ligand, but an identical interaction pattern. In light of our docking studies into the hERG potassium channel, we developed an algorithm (ROTALI) to detect the poses that are duplicates due to the symmetry of the channel. This led to a reduction in the number of poses to be considered in the subsequent steps by up to 52%.
Keywords: Symmetric Binding site; Docking; Duplicate poses; hERG Symmetric Binding site; Docking; Duplicate poses; hERG
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Share & Cite This Article

MDPI and ACS Style

SCHIESARO, A.; RICHTER, L.; ECKER, G.F. How to Solve the Problems of Docking into a Symmetric Binding Site: The Example of the hERG Channel. Sci. Pharm. 2013, 81, 677-682.

Show more citation formats Show less citations formats

Article Metrics

Article Access Statistics



[Return to top]
Sci. Pharm. EISSN 2218-0532 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top