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A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories

Molecular and Cellular Modeling

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Abstract

Not specified

Authors: Daria B. Kokh, Bernd Doser, Stefan Richter, Fabian Ormersbach, Xingyi Cheng, Rebecca C. Wade

Date Published: 28th Sep 2020

Publication Type: Journal

DOI: 10.1063/5.0019088

Citation: J. Chem. Phys. 153(12):125102

Created: 27th Sep 2020 at 07:47, Last updated: 5th Mar 2024 at 21:24

Druggability Assessment in TRAPP Using Machine Learning Approaches

Molecular and Cellular Modeling

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Abstract

Not specified

Authors: Jui-Hung Yuan, Sungho Bosco Han, Stefan Richter, Rebecca C. Wade, Daria B. Kokh

Date Published: 23rd Mar 2020

Publication Type: Journal

DOI: 10.1021/acs.jcim.9b01185

Citation: J. Chem. Inf. Model. 60(3):1685-1699

Created: 2nd Mar 2020 at 16:26, Last updated: 5th Mar 2024 at 21:24

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.

Molecular and Cellular Modeling

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Abstract

Not specified

Authors: Antonia Stank, Daria B. Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C. Wade

Date Published: 3rd Jul 2017

Publication Type: Journal

DOI: 10.1093/nar/gkx277

Citation: Nucleic Acids Research 45(W1):W325-W330

Created: 7th Sep 2019 at 11:39, Last updated: 5th Mar 2024 at 21:23

Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer

Molecular and Cellular Modeling

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Abstract

Not specified

Authors: Xiaofeng Yu, Daria B. Kokh, Prajwal Nandekar, Ghulam Mustafa, Stefan Richter, Rebecca C. Wade

Date Published: 2016

Publication Type: InCollection

DOI: 10.1007/978-3-319-24633-8_17

Citation: High Performance Computing in Science and Engineering ´15,pp.255-264,Springer International Publishing

Created: 7th Sep 2019 at 08:19, Last updated: 5th Mar 2024 at 21:23

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

Molecular and Cellular Modeling

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Abstract

Not specified

Authors: Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter, Rebecca C. Wade

Date Published: 5th Aug 2015

Publication Type: Journal

DOI: 10.1002/jcc.23971

Citation: J. Comput. Chem. 36(21):1631-1645

Created: 6th Dec 2019 at 13:49, Last updated: 5th Mar 2024 at 21:24

TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins

Molecular and Cellular Modeling

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Abstract

Not specified

Authors: Daria B. Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade

Date Published: 24th Apr 2013

Publication Type: Journal

DOI: 10.1021/ci4000294

Citation: J. Chem. Inf. Model. 53(5):1235-1252

Created: 6th Dec 2019 at 15:07, Last updated: 5th Mar 2024 at 21:24

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