tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling

no code implementations • 27 Feb 2024 • Thomas-Otavio Peulen, Katherina Hemmen, Annemarie Greife, Benjamin M. Webb, Suren Felekyan, Andrej Sali, Claus A. M. Seidel, Hugo Sanabria, Katrin G. Heinze

We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines that unifies various spectroscopic analysis tools.

The FRET-based structural dynamics challenge -- community contributions to consistent and open science practices

no code implementations • 4 Jun 2020 • Eitan Lerner, Benjamin Ambrose, Anders Barth, Victoria Birkedal, Scott C. Blanchard, Richard Borner, Thorben Cordes, Timothy D. Craggs, Taekjip Ha, Gilad Haran, Thorsten Hugel, Antonino Ingargiola, Achillefs Kapanidis, Don C. Lamb, Ted Laurence, Nam ki Lee, Edward A. Lemke, Emmanuel Margeat, Jens Michaelis, Xavier Michalet, Daniel Nettels, Thomas-Otavio Peulen, Benjamin Schuler, Claus A. M. Seidel, Hamid So-leimaninejad, Shimon Weiss

These recent efforts include multi-lab blind-tests to assess the accuracy and precision of smFRET between different labs using different procedures, the formal assembly of the FRET community and development of smFRET procedures to be considered for entries in the wwPDB.

Position

Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation

no code implementations • 17 Dec 2018 • Maksym Tsytlonok, Hugo Sanabria, Yuefeng Wang, Suren Felekyan, Katherina Hemmen, Aaron Phillips, Mi-Kyung Yun, Brett Waddell, Cheon-Gil Park, Sivaraja Vaithiyalingam, Luigi Iconaru, Stephen W. White, Peter Tompa, Claus A. M. Seidel, Richard Kriwacki

p27$^{Kip1}$ (p27) is an intrinsically disordered protein (IDP) that folds upon binding to cyclin-dependent kinase (Cdk)$/$cyclin complexes (e. g., Cdk2$/$cyclin A), inhibiting their catalytic activity and causing cell cycle arrest.