Daria B. Kokh: search on Z-Library

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1

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci, Musa, Kokh, Daria B., Corni, Stefano, Wade, Rebecca C.

Journal:

Quarterly Reviews of Biophysics

Year:

2016

Language:

english

File:

PDF, 1.36 MB

english, 2016

2

Receptor flexibility in small-molecule docking calculations

Daria B. Kokh, Rebecca C. Wade, Wolfgang Wenzel

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2011

Language:

english

File:

PDF, 542 KB

english, 2011

3

Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

Schuetz, Doris A., de Witte, Wilhelmus Egbertus Arnout, Wong, Yin Cheong, Knasmueller, Bernhard, Richter, Lars, Kokh, Daria B., Sadiq, S. Kashif, Bosma, Reggie, Nederpelt, Indira, Heitman, Laura H., S

Journal:

Drug Discovery Today

Year:

2017

Language:

english

File:

PDF, 937 KB

english, 2017

4

New approaches for computing ligand–receptor binding kinetics

Bruce, Neil J, Ganotra, Gaurav K, Kokh, Daria B, Sadiq, S Kashif, Wade, Rebecca C

Journal:

Current Opinion in Structural Biology

Year:

2018

Language:

english

File:

PDF, 1.42 MB

english, 2018

5

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

Kokh, Daria B., Amaral, Marta, Bomke, Joerg, Grädler, Ulrich, Musil, Djordje, Buchstaller, Hans-Peter, Dreyer, Matthias K., Frech, Matthias, Lowinski, Maryse, Vallee, Francois, Bianciotto, Marc, Rak,

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 5.98 MB

english, 2018

6

Recent progress in molecular simulation methods for drug binding kinetics

Nunes-Alves, Ariane, Kokh, Daria B, Wade, Rebecca C

Journal:

Current Opinion in Structural Biology

Year:

2020

File:

PDF, 1.67 MB

2020

7

A Quantitative, Real-Time Assessment of Binding of Peptides and Proteins to Gold Surfaces

Ori Cohavi, Dr. Dana Reichmann, Renne Abramovich, Alexander B. Tesler, Dr. Giuliano Bellapadrona, Dr. Daria B. Kokh, Dr. Rebecca C. Wade, Dr. Alexander Vaskevich, Prof. Israel Rubinstein, Prof. Gideon

Journal:

Chemistry - A European Journal

Year:

2011

Language:

english

File:

PDF, 639 KB

english, 2011

8

Protein–surface interactions: challenging experiments and computations

Ori Cohavi, Stefano Corni, Francesca De Rienzo, Rosa Di Felice, Kay E. Gottschalk, Martin Hoefling, Daria Kokh, Elisa Molinari, Gideon Schreiber, Alexander Vaskevich, Rebecca C. Wade

Journal:

Journal of Molecular Recognition

Year:

2010

Language:

english

File:

PDF, 82 KB

english, 2010

9

High throughput in-silico screening against flexible protein receptors

Horacio Pérez-Sánchez, Bernhard Fischer, Daria Kokh, Holger Merlitz, Wolfgang Wenzel

Journal:

Journal of Cheminformatics

Year:

2010

Language:

english

File:

PDF, 147 KB

english, 2010

10

Diffusion and association processes in biological systems: theory, computation and experiment

Paolo Mereghetti, Daria Kokh, J Andrew McCammon, Rebecca C Wade

Journal:

Year:

2011

Language:

english

File:

PDF, 198 KB

english, 2011

11

Trends in adsorption of open-shell atoms and small molecular fragments on the Ag(1 1 1) surface

Daria B. Kokh, Robert J. Buenker, Jerry L. Whitten

Journal:

Surface Science

Year:

2006

Language:

english

File:

PDF, 463 KB

english, 2006

12

Docking of Ubiquitin to Gold Nanoparticles

Brancolini, Giorgia, Kokh, Daria B., Calzolai, Luigi, Wade, Rebecca C., Corni, Stefano

Journal:

Year:

2012

Language:

english

File:

PDF, 2.09 MB

english, 2012

13

TRAPP: A Tool for Analysis of Tra nsient Binding P ockets in P roteins

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

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 3.45 MB

english, 2013

14

Theoretical study of the UV photodissociation of Cl[sub 2]: Potentials, transition moments, extinction coefficients, and Cl∗/Cl branching ratio

Kokh, Daria B., Alekseyev, Aleksey B., Buenker, Robert J.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 445 KB

english, 2004

15

Modeling of Protein Adsorption on a Metal Surface: Brownian Dynamics Simulations

Kokh, Daria B., Huang, Bingding, Wade, Rebecca C., Winn, Peter J.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 53 KB

english, 2009

16

ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent

Kokh, Daria B., Corni, Stefano, Winn, Peter J., Hoefling, Martin, Gottschalk, Kay E., Wade, Rebecca C.

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

17

Flexible Side Chain Models Improve Enrichment Rates in In Silico Screening

Kokh, Daria B., Wenzel, Wolfgang

Journal:

Journal of Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 3.06 MB

english, 2008

18

HI Photofragmentation Revisited. Comment on “Probing Excited Electronic States Using Vibrationally Mediated Photolysis: Application to Hydrogen Iodide”

Alekseyev, Aleksey B., Kokh, Daria B., Buenker, Robert J.

Journal:

Journal of Physical Chemistry A

Year:

2005

Language:

english

File:

PDF, 78 KB

english, 2005

19

Nonadiabatic effects in the lowest 0[sup +]([sup 3]P) ion-pair states of CIF

Kokh, Daria B., Li, Yan, Buenker, Robert J., Alekseyev, Aleksey B., Liebermann, Heinz-Peter, Alekseev, Vadim A.

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 353 KB

english, 2001

20

Relativistic configuration interaction study of the ClF molecule and its emission spectra from 0+ ion-pair states

Alekseyev, Aleksey B., Liebermann, Heinz-Peter, Buenker, Robert J., Kokh, Daria B.

Journal:

The Journal of Chemical Physics

Year:

2000

Language:

english

File:

PDF, 432 KB

english, 2000

21

The lowest 1([sup 3]P[sub J]) and 2([sup 3]P[sub 2]) ion-pair states of ClF: Nonadiabatic effects and emission spectra

Kokh, Daria B., Alekseyev, Aleksey B., Li, Yan, Buenker, Robert J.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 378 KB

english, 2002

22

On the ultraviolet photofragmentation of hydrogen iodide

Alekseyev, Aleksey B., Liebermann, Heinz-Peter, Kokh, Daria B., Buenker, Robert J.

Journal:

The Journal of Chemical Physics

Year:

2000

Language:

english

File:

PDF, 397 KB

english, 2000

23

Photodissociation of CH[sub 3]Cl, C[sub 2]H[sub 5]Cl, and C[sub 6]H[sub 5]Cl on the Ag(111) surface: Ab initio embedded cluster and configuration interaction study

Kokh, Daria B., Liebermann, Heinz-Peter, Buenker, Robert J.

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 894 KB

english, 2010

24

When the label matters: Adsorption of labelled and unlabelled proteins on charged surfaces

Romanowska, Julia, Kokh, Daria B., Wade, Rebecca C

Journal:

Year:

2015

Language:

english

File:

PDF, 1.61 MB

english, 2015

25

Theoretical Study of the CH 2 + O Photodissociation of Formaldehyde Adsorbed on the Ag(111) Surface

Kokh, Daria B., Buenker, Robert J., Liebermann, Heinz-Peter, Pichl, Lukáš, Whitten, Jerry L.

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 433 KB

english, 2005

26

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

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

Journal:

Journal of Computational Chemistry

Year:

2015

Language:

english

File:

PDF, 911 KB

english, 2015

27

Protein Binding Pocket Dynamics

Stank, Antonia, Kokh, Daria B., Fuller, Jonathan C., Wade, Rebecca C.

Journal:

Accounts of Chemical Research

Year:

2016

Language:

english

File:

PDF, 2.55 MB

english, 2016

28

Theoretical Study of the Photoinduced C−H Bond Cleavage in Formaldehyde Adsorbed on the Ag(111) Surface

Kokh, Daria B., Buenker, Robert J., Liebermann, Heinz-Peter, Whitten, Jerry L.

Journal:

The Journal of Physical Chemistry C

Year:

2007

Language:

english

File:

PDF, 232 KB

english, 2007

29

Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets

Kokh, Daria B., Czodrowski, Paul, Rippmann, Friedrich, Wade, Rebecca C

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 1.99 MB

english, 2016

30

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

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

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 1.74 MB

english, 2017

31

Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times

Kokh, Daria B., Kaufmann, Tom, Kister, Bastian, Wade, Rebecca C.

Journal:

Frontiers in Molecular Biosciences

Year:

2019

Language:

english

File:

PDF, 7.23 MB

english, 2019

32

Druggability Assessment in TRAPP using Machine Learning Approaches

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

Journal:

Journal of Chemical Information and Modeling

Year:

2020

Language:

english

File:

PDF, 5.67 MB

english, 2020

33

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

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

Journal:

The Journal of Chemical Physics

Year:

2020

File:

PDF, 5.28 MB

2020