Kokh, Daria B. Dr.Universität HeidelbergHeidelberg
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Co-Autoren (Uni Heidelberg)
Co-Autoren (extern)
- Knapp, Stefan (1)
- Gkeka, Paraskevi (1)
- Henrich, Stefan (1)
- Martinez, Michael (1)
- Rippmann, Friedrich (1)
- Czodrowski, Paul (1)
- Fuller, Jonathan C. (1)
- Bruce, Neil J. (1)
- Nunes-Alves, Ariane (1)
- Corni, Stefano (1)
- Romanowska, Julia (1)
- Doser, Bernd (1)
- Cheng, Xingyi (1)
- Berger, Benedict-Tilman (1)
- Nunes-Alves, Ariane (1)
- Neil, Rebecca (1)
- Navratilova, Iva (1)
- Musil, Djordje (1)
- Müller, Susanne (1)
- Elkins, Jonathan M. (1)
- Bomke, Joerg (1)
- Ormersbach, Fabian (1)
- Czodrowski, Paul (1)
- Bianciotto, Marc (1)
- Minoux, Hervé (1)
Publikationen in heiBIB 
- Bianciotto, Marc: Contact map fingerprints of protein-ligand unbinding trajectories reveal mechanisms determining residence times computed from scaled molecular dynamics / Marc Bianciotto, Paraskevi Gkeka, Daria B. Kokh, Rebecca C. Wade, and Hervé Minoux, September 8, 2021. - 14 S.
In: Journal of chemical theory and computation, ISSN 1549-9626. 17(2021), 10, Seite 6522-6535
DOI: 10.1021/acs.jctc.1c00453
- Kokh, Daria B.: G protein-coupled receptor-ligand dissociation rates and mechanisms from τRAMD simulations / Daria B. Kokh and Rebecca C. Wade, September 8, 2021. - 14 S.
In: Journal of chemical theory and computation, ISSN 1549-9626. 17(2021), 10 vom: Okt., Seite 6610-6623
DOI: 10.1021/acs.jctc.1c00641
- Reinhardt, Martin: Brownian dynamics simulations of proteins in the presence of surfaces : Long-Range Electrostatics and Mean-Field Hydrodynamics / Martin Reinhardt, Neil J. Bruce, Daria B. Kokh, and Rebecca C. Wade, 8 June 2021. - 15 S.
In: Journal of chemical theory and computation, ISSN 1549-9626. 17(2021), 6, Seite 3510-3524
DOI: 10.1021/acs.jctc.0c01312
- Berger, Benedict-Tilman: Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2 / Benedict-Tilman Berger, Marta Amaral, Daria B. Kokh, Ariane Nunes-Alves, Djordje Musil, Timo Heinric… , January 25, 2021. - 20 S.
In: Cell chemical biology, ISSN 2451-9448. 28(2021), 5 vom: Mai, Seite 686-698.e1-e7
DOI: 10.1016/j.chembiol.2021.01.003
- Yuan, Jui-Hung: Druggability assessment in TRAPP using machine learning approaches / Jui-Hung Yuan, Sungho Bosco Han, Stefan Richter, Rebecca C. Wade and Daria B. Kokh, 27 February 2020. - 15 S.
In: Journal of chemical information and modeling, ISSN 1549-960X. 60(2020), 3, Seite 1685-1699
DOI: 10.1021/acs.jcim.9b01185
- Nunes-Alves, Ariane: Recent progress in molecular simulation methods for drug binding kinetics / Ariane Nunes-Alves, Daria B Kokh and Rebecca C Wade, 6 August 2020. - 8 S.
In: Current opinion in structural biology. 64(2020), Seite 126-133
DOI: 10.1016/j.sbi.2020.06.022
- Kokh, Daria B.: A workflow for exploring ligand dissociation from a macromolecule : efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories / Daria B. Kokh, Bernd Doser, Stefan Richter, Fabian Ormersbach, Xingyi Cheng, and Rebecca C. Wade, 25 September 2020
In: The journal of chemical physics, ISSN 1089-7690. 153(2020,12) Artikel-Nummer 125102, 15 Seiten
DOI: 10.1063/5.0019088
- Kokh, Daria B.: Machine learning analysis of [tau]RAMD trajectories to decipher molecular determinants of drug-target residence times / Daria B. Kokh, Tom Kaufmann, Bastian Kister, Rebecca C. Wade, 24 May 2019. - 17 S.
In: Frontiers in molecular biosciences, ISSN 2296-889X. 6(2019) Artikel-Nummer 36, 17 Seiten
DOI: 10.3389/fmolb.2019.00036
- Kokh, Daria B.: Estimation of drug-target residence times by t-random acceleration molecular dynamics simulations / Daria B. Kokh, Marta Amaral, Joerg Bomke, Ulrich Grädler, Djordje Musil, Hans-Peter Buchstaller, Mat… , 16 May 2018. - 11 S.
In: Journal of chemical theory and computation, ISSN 1549-9626. 14(2018), 7, Seite 3859-3869
DOI: 10.1021/acs.jctc.8b00230
- Schuetz, Doris A.: Kinetics for drug discovery : an industry-driven effort to target drug residence time / Doris A. Schuetz, Wilhelmus Egbertus Arnout de Witte, Yin Cheong Wong, Bernhard Knasmueller, Lars Ri… , 2017, Apr 13. - 16 S.
In: Drug discovery today, ISSN 1878-5832. 22(2017), 6, Seite 896-911
DOI: 10.1016/j.drudis.2017.02.002
- Amaral, Marta: Protein conformational flexibility modulates kinetics and thermodynamics of drug binding / M. Amaral, D.B. Kokh, J. Bomke, A. Wegener, H.P. Buchstaller, H.M. Eggenweiler, P. Matias, C. Sirren… , 22 December 2017. - 14 S.
In: Nature Communications, ISSN 2041-1723. 8(2017) Artikel-Nummer 2276, 14 Seiten
DOI: 10.1038/s41467-017-02258-w
- Özboyacı, Musa: Three steps to gold : mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations / M. Ozboyaci, D.B. Kokh and R.C. Wade, 21 Mar 2016. - 10 S.
In: Physical chemistry, chemical physics, ISSN 1463-9084. 18(2016), 15, Seite 10191-10200
DOI: 10.1039/C6CP00201C
- Özboyacı, Musa: Modeling and simulation of protein-surface interactions : achievements and challenges / Musa Ozboyaci, Daria B. Kokh, Stefano Corni and Rebecca C. Wade, 29 January 2016. - 45 S.
In: Quarterly reviews of biophysics, ISSN 1469-8994. 49(2016) Artikel-Nummer e4, 45 Seiten
DOI: 10.1017/S0033583515000256
- Stank, Antonia: Protein binding pocket dynamics / Antonia Stank, Daria B. Kokh, Jonathan C. Fuller, and Rebecca C. Wade, April 25, 2016. - 7 S.
In: Accounts of chemical research, ISSN 1520-4898. 49(2016), 5, Seite 809-815
DOI: 10.1021/acs.accounts.5b00516
- Kokh, Daria B.: Perturbation approaches for exploring protein binding site flexibility to predict transient binding pockets / Daria B. Kokh, Paul Czodrowski, Friedrich Rippmann and Rebecca C. Wade, July 11, 2016. - 14 S.
In: Journal of chemical theory and computation, ISSN 1549-9626. 12(2016), 8, Seite 4100-4113
DOI: 10.1021/acs.jctc.6b00101
- Romanowska, Julia: When the label matters : adsorption of labeled and unlabeled proteins on charged surfaces / Julia Romanowska, Daria B. Kokh, Rebecca C. Wade, October 22, 2015. - 6 S. : Illustrationen
In: Nano letters, ISSN 1530-6992. 15(2015), 11, Seite 7508-7513
DOI: 10.1021/acs.nanolett.5b03168
- Martinez, Michael: SDA 7 : a modular and parallel implementation of the simulation of diffusional association software / Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet… , 29 June 2015. - 15 S.
In: Journal of computational chemistry, ISSN 1096-987X. 36(2015), 21, Seite 1631-1645
DOI: 10.1002/jcc.23971
- Kokh, Daria B.: TRAPP : a tool for analysis of Transient binding Pockets in Proteins / Daria B. Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann, and Rebecca C. W… , April 27, 2013. - 18 S.
In: Journal of chemical information and modeling, ISSN 1549-960X. 53(2013), 5, Seite 1235-1252
DOI: 10.1021/ci4000294
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