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453 Publications visible to you, out of a total of 453
Computing Protein-Ligand Binding Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics Simulations

Abstract

Not specified

Authors: S Kashif Sadiq, Rebecca C Wade

Date Published: 2018

Publication Type: Journal

A novel method to treat gated protein-ligand binding via on-the-fly conformational updates within rigid body BD simulations

Abstract

Not specified

Author: Patrick Friedrich

Date Published: 2018

Publication Type: Master's Thesis

A computational approach to decipher chromatosome structure determinants

Abstract

Not specified

Author: Mehmet Ali Öztuerk

Date Published: 2018

Publication Type: Doctoral Thesis

Modelling of Neurotrophin Receptors

Abstract

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Author: Jan-Niklas Dohrke

Date Published: 2018

Publication Type: Bachelor's Thesis

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding

Abstract (Expand)

Structure-based drug design has often been restricted by the rather static picture of protein–ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibility …y in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery.

Authors: M. Amaral, D. B. Kokh, J. Bomke, A. Wegener, H. P. Buchstaller, H. M. Eggenweiler, P. Matias, C. Sirrenberg, R. C. Wade, M. Frech

Date Published: 1st Dec 2017

Publication Type: Journal

Early career researchers want Open Science

Abstract (Expand)

Open Science is encouraged by the European Union and many other political and scientific institutions. However, scientific practice is proving slow to change. We propose, as early career researchers, … that it is our task to change scientific research into open scientific research and commit to Open Science principles.

Authors: Andrea Farnham, Christoph Kurz, Mehmet Ali Öztürk, Monica Solbiati, Oona Myllyntaus, Jordy Meekes, Tra My Pham, Clara Paz, Magda Langiewicz, Sophie Andrews, Liisa Kanninen, Chantal Agbemabiese, Arzu Tugce Guler, Jeffrey Durieux, Sarah Jasim, Olivia Viessmann, Stefano Frattini, Danagul Yembergenova, Carla Marin Benito, Marion Porte, Anaïs Grangeray-Vilmint, Rafael Prieto Curiel, Carin Rehncrona, Tareq Malas, Flavia Esposito, Kristina Hettne

Date Published: 1st Dec 2017

Publication Type: Journal

Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors

Abstract

Not specified

Authors: Joanna Panecka-Hofman, Ina Pöhner, Francesca Spyrakis, Talia Zeppelin, Flavio Di Pisa, Lucia Dello Iacono, Alessio Bonucci, Antonio Quotadamo, Alberto Venturelli, Stefano Mangani, Maria Paola Costi, Rebecca C. Wade

Date Published: 1st Dec 2017

Publication Type: Journal

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