D. Kokh

发表

A quantitative, real-time assessment of binding of peptides and proteins to gold surfaces.

Gideon Schreiber, Rebecca C. Wade, Daria B. Kokh, 2011, Chemistry.

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

R. Wade, M. Frech, M. Dreyer, 2018, Journal of chemical theory and computation.

New approaches for computing ligand-receptor binding kinetics.

Neil J. Bruce, R. Wade, S. Sadiq, 2018, Current opinion in structural biology.

Computational Approaches for Studying Drug Binding Kinetics

Jonathan C. Fuller, R. Wade, J. Romanowska, 2015 .

Protein Binding Pocket Dynamics.

Jonathan C. Fuller, R. Wade, D. Kokh, 2016, Accounts of chemical research.

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

Leigh A. Stoddart, R. Wade, R. Leurs, 2017, Drug discovery today.

Docking of ubiquitin to gold nanoparticles.

Luigi Calzolai, Daria B Kokh, Rebecca C Wade, 2012, ACS nano.

A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics

R. Wade, E. Lindahl, F. Spyrakis, 2020, bioRxiv.

Spectroscopic determination of the cold electron population in very low pressure ECR discharges in N2/He mixtures

N. Bibinov, D. Kokh, K. Wiesemann, 2005 .

A comparative study of the electron distribution function in the positive columns in and /He dc glow discharges by optical spectroscopy and probes

N. Bibinov, D. Kokh, N. B. Kolokolov, 1998 .

Theoretical study of the UV photodissociation of Cl2: potentials, transition moments, extinction coefficients, and Cl*/Cl branching ratio.

D. Kokh, A. B. Alekseyev, R. Buenker, 2004, The Journal of chemical physics.

Absolute calibration of the efficiency of a VUV-monochromator/detector system in the range 110 - 450 nm

N. Bibinov, D. Kokh, A. Pravilov, 1997 .

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

R. Wade, D. Kokh, G. Mustafa, 2016 .

Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics.

Neil J. Bruce, R. Wade, M. Reinhardt, 2020, Journal of chemical theory and computation.

Supporting Information: Graphene BioFET sensors for SARS-CoV-2 detection: A multiscale approach

R. Wade, D. Kokh, E. G. Marín, 2022 .

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

R. Wade, D. Kokh, B. Doser, 2020, The Journal of chemical physics.

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

D. Kokh, J. Whitten, R. Buenker, 2006 .

The vibrationally mediated photodissociation of Cl2.

Alex Brown, B. Winter, D. Kokh, 2012, The Journal of chemical physics.

Photodissociation of CH3Cl, C2H5Cl, and C6H5Cl on the Ag(111) surface: ab initio embedded cluster and configuration interaction study.

D. Kokh, H. Liebermann, R. Buenker, 2010, The Journal of chemical physics.

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

D. Kokh, J. Whitten, H. Liebermann, 2007 .

Protein–surface interactions: challenging experiments and computations

Gideon Schreiber, Martin Hoefling, Rosa Di Felice, 2009, Journal of molecular recognition : JMR.

Theoretical study of the CH2 + O photodissociation of formaldehyde adsorbed on the Ag(111) surface.

L. Pichl, D. Kokh, J. Whitten, 2005, The journal of physical chemistry. B.

Electric dipole moment function of the beta 1(3P2)toA 1 3Pi transition in ICl

N. Bibinov, D. Kokh, A. Pravilov, 1999 .

Ab initio study of spectroscopic and radiative characteristics of ion-pair states of the Cl2 molecule

D. Kokh, A. B. Alekseyev, R. Buenker, 2001 .

Optical transitions from the chlorine (3P2) ion-pair state

N. Bibinov, D. Kokh, A. Fateev, 2000 .

The transition dipole moment function of the chlorine E0g+(3P2)−B3Π0u+ system

N. Bibinov, D. Kokh, A. Fateev, 1998 .

Study of the covalent and triplet ionic-pairing states of the fluorine molecule with the MRDCI method

D. Kokh, A. Pravilov, I. A. Delyagina, 2003 .

On the ultraviolet photofragmentation of hydrogen iodide

D. Kokh, A. B. Alekseyev, H. Liebermann, 2000 .

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

D. Kokh, A. B. Alekseyev, H. Liebermann, 2000 .

HI photofragmentation revisited. Comment on "Probing excited electronic states using vibrationally mediated photolysis: Application to hydrogen iodide".

D. Kokh, A. B. Alekseyev, R. Buenker, 2005, The journal of physical chemistry. A.

The iodine E0g+–B0u+ and D0u+–X0g+ transition dipole moment functions

N. Bibinov, D. Kokh, A. Pravilov, 1999 .

The approach-induced I2() transitions, M=He, Ar, I2, N2, CF4

N. Bibinov, D. Kokh, A. Pravilov, 2001 .

The `approach-induced' transition

O. Vasyutinskii, N. Bibinov, D. Kokh, 1999 .

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

Friedrich Rippmann, Stefan Richter, Rebecca C. Wade, 2013, J. Chem. Inf. Model..

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

Stefan Richter, Rebecca C. Wade, Musa Ozboyaci, 2015, J. Comput. Chem..

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding

R. Wade, M. Frech, J. Bomke, 2017, Nature Communications.

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

Stefan Richter, Rebecca C. Wade, Max Horn, 2017, Nucleic Acids Res..

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

Friedrich Rippmann, Daria B Kokh, Rebecca C Wade, 2016, Journal of chemical theory and computation.

Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2.

R. Wade, S. Knapp, J. Elkins, 2021, Cell chemical biology.

High throughput in-silico screening against flexible protein receptors

Wolfgang Wenzel, Holger Merlitz, Bernhard Fischer, 2010, J. Cheminformatics.

A complete quantum mechanical study of chlorine photodissociation.

Alex Brown, D. Kokh, M. Brouard, 2012, The Journal of chemical physics.

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding

R. Wade, M. Frech, P. Matias, 2017, Nature Communications.

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

Daria B Kokh, Rebecca C Wade, Musa Ozboyaci, 2016, Quarterly Reviews of Biophysics.

Recent progress in molecular simulation methods for drug binding kinetics.

Daria B. Kokh, Rebecca C. Wade, Ariane Nunes-Alves, 2020, Current opinion in structural biology.

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

Daria B. Kokh, Tom Kaufmann, Bastian Kister, 2019, Front. Mol. Biosci..

Flexible side chain models improve enrichment rates in in silico screening.

Wolfgang Wenzel, Daria B Kokh, W. Wenzel, 2008, Journal of medicinal chemistry.

Impact of Induced Fit on Ligand Scoring and a Strategy of Identifying a Minimal Set of Flexible Residues

J. Neumann, S. Mohanty, W. Wenzel, 2008 .

Electronic polarization effects in the photodissociation of Cl2.

Alex Brown, B. Winter, D. Kokh, 2012, The Journal of chemical physics.

Graphene BioFET sensors for SARS-CoV-2 detection: a multiscale simulation approach

R. Wade, D. Kokh, E. G. Marín, 2022, Nanoscale Advances.

G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from τRAMD Simulations.

R. Wade, D. Kokh, 2021, Journal of chemical theory and computation.

G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from τRAMD Simulations

R. Wade, D. Kokh, 2021, bioRxiv.

SPECTROSCOPIC DETERMINATION OF COLD ELECTRONS IN ELECTRON CYCLOTRON RESONANCE DISCHARGES WITH HIGHLY CHARGED IONS

N. Bibinov, D. Kokh, K. Wiesemann, 1998 .

Receptor flexibility in small‐molecule docking calculations

Wolfgang Wenzel, Daria B. Kokh, Rebecca C. Wade, 2011 .

Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations.

R. Wade, M. Ozboyaci, D. Kokh, 2016, Physical chemistry chemical physics : PCCP.

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

J Andrew McCammon, Rebecca C Wade, Paolo Mereghetti, 2011, BMC biophysics.

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

Martin Hoefling, Daria B Kokh, Rebecca C Wade, 2010, Journal of chemical theory and computation.

Contact Map Fingerprints of Protein-Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics.

R. Wade, H. Minoux, P. Gkeka, 2021, Journal of chemical theory and computation.

When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces.

R. Wade, J. Romanowska, D. Kokh, 2015, Nano letters.

Druggability Assessment in TRAPP using Machine Learning Approaches

Stefan Richter, Jui-Hung Yuan, Sungho Bosco Han, 2019, bioRxiv.

Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations

R. Wade, D. Kokh, Ariane Nunes-Alves, 2020, Current research in structural biology.

Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics

Lucas G. Viviani, R. Wade, D. Kokh, 2023, J. Chem. Inf. Model..

Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations.

D. Kokh, Musa Ozboyaci, Rebecca C. Wade, 2016, Physical chemistry chemical physics : PCCP.

Configuration interaction study of the excited states of CO adsorbed on a Pt97 cluster

E. Izgorodina, D. Kokh, J. Whitten, 2003 .

Protein Binding Pocket Dynamics.

Jonathan C. Fuller, R. Wade, D. Kokh, 2016, Accounts of chemical research.

Protein–surface interactions: challenging experiments and computations

R. Wade, A. Vaskevich, E. Molinari, 2009, Journal of molecular recognition : JMR.

Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD

D. Kokh, Ariane Nunes-Alves, Giulia D’Arrigo, 2024, bioRxiv.

Structure-Kinetic-Relationship Reveals the Mechanism of Selectivity of FAK Inhibitors Over PYK2

R. Wade, S. Knapp, J. Elkins, 2020 .

Comprehensive characterization of ligand unbinding mechanisms and kinetics for T4 lysozyme mutants using tauRAMD

R. Wade, D. Kokh, Ariane Nunes-Alves, 2020, 2010.08763.