New version of TRAPP released

4. November 2021

Researchers from the Molecular and Cellular Modeling (MCM) group at HITS released a new version of the TRAnsient Pockets in Proteins (TRAPP) webserver, available at https://trapp.h-its.org/.

The main new feature in TRAPP version 4 is the use of machine learning and molecular simulation to predict druggability, i.e. the ability to bind to a drug-like compound, of the protein binding site studied. In such a way, TRAPP facilitates the discovery of cryptic binding pockets that may not be apparent in the experimentally determined structure of a protein but that can be revealed when the protein motions are simulated.

The druggability score can help the user to easily identify the most druggable conformation of a given binding pocket from a set of conformations obtained from experiments or a molecular dynamics simulation.  This predicted druggable conformation can then be used for drug design. TRAPP also includes visualization tools that enable the user to identify the factors affecting the predicted druggability of protein binding pockets.

References:

Jui-Hung Yuan, Sungho Bosco Han, Stefan Richter, Rebecca C Wade, Daria B. Kokh
Druggability Assessment in TRAPP using Machine Learning Approaches
JYuan J, Han SB, Richter S, Wade RC, Kokh DB (2020). Druggability Assessment in TRAPP Using Machine Learning Approaches, J. Chem. Inf. Model. 60(3):1685-1699 1

Stank A, Kokh DB, Horn M, Sizikova E, Neil R, Panecka J, Richter S, Wade RC (2017). TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets., Nucleic Acids Research 45(W1):W325-W330

Kokh DB, Richter S, Henrich S, Czodrowski P, Rippmann F, Wade RC (2013). TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins, J. Chem. Inf. Model. 53(5):1235-1252

About HITS

The Heidelberg Institute for Theoretical Studies (HITS) was established in 2010 by the physicist and SAP co-founder Klaus Tschira (1940-2015) and the Klaus Tschira Foundation as a private, non-profit research institute. HITS conducts basic research in the natural sciences, mathematics and computer science, with a focus on the processing, structuring, and analyzing of large amounts of complex data and the development of computational methods and software. The research fields range from molecular biology to astrophysics. The shareholders of HITS are the HITS-Stiftung, which is a subsidiary of the Klaus Tschira Foundation, Heidelberg University and the Karlsruhe Institute of Technology (KIT). HITS also cooperates with other universities and research institutes and with industrial partners. The base funding of HITS is provided by the HITS Stiftung with funds received from the Klaus Tschira Foundation. The primary external funding agencies are the Federal Ministry of Education and Research (BMBF), the German Research Foundation (DFG), and the European Union.

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