User profiles for Daria B. Kokh

Daria B. Kokh

Cancer Registry of Baden-Württemberg
Verified email at klr-krbw.de
Cited by 3116

Protein binding pocket dynamics

A Stank, DB Kokh, JC Fuller… - Accounts of chemical …, 2016 - ACS Publications
Conspectus The dynamics of protein binding pockets are crucial for their interaction specificity.
Structural flexibility allows proteins to adapt to their individual molecular binding partners …

Estimation of drug-target residence times by τ-random acceleration molecular dynamics simulations

DB Kokh, M Amaral, J Bomke, U Grädler… - Journal of chemical …, 2018 - ACS Publications
Drug-target residence time (τ), one of the main determinants of drug efficacy, remains highly
challenging to predict computationally and, therefore, is usually not considered in the early …

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

M Ozboyaci, DB Kokh, S Corni… - Quarterly reviews of …, 2016 - cambridge.org
Understanding protein–inorganic surface interactions is central to the rational design of new
tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant …

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

…, YC Wong, B Knasmueller, L Richter, DB Kokh… - Drug Discovery …, 2017 - Elsevier
… 3b) and the affinity and dissociation rate constants were highly correlated between both …
(b) Different strategies required for improvement of K D , k on and k off values (yellow, orange …

Docking of ubiquitin to gold nanoparticles

G Brancolini, DB Kokh, L Calzolai, RC Wade, S Corni - ACS nano, 2012 - ACS Publications
Protein–nanoparticle associations have important applications in nanoscience and
nanotechnology such as targeted drug delivery and theranostics. However, the mechanisms by …

New approaches for computing ligand–receptor binding kinetics

NJ Bruce, GK Ganotra, DB Kokh, SK Sadiq… - Current opinion in …, 2018 - Elsevier
… Author links open overlay panel Neil J Bruce 1 4 , Gaurav K Ganotra 1 3 4 , Daria B Kokh 1
… N-terminal domain of HSP90 and of focal adhesion kinase (Kokh et al., unpublished data). …

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

DB Kokh, B Doser, S Richter, F Ormersbach… - The Journal of …, 2020 - pubs.aip.org
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide
range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far …

Recent progress in molecular simulation methods for drug binding kinetics

A Nunes-Alves, DB Kokh, RC Wade - Current Opinion in Structural Biology, 2020 - Elsevier
… Author links open overlay panel Ariane Nunes-Alves 1 2 4 , Daria B Kokh 1 4 , Rebecca C
… (B): Plot of k off vs k on for 104 HSP90 inhibitors [28]. Cyan: helix-binders, magenta: loop-…

A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics

…, P Carloni, RC Wade, F Musiani, DB Kokh… - ACS pharmacology & …, 2021 - ACS Publications
The SARS-CoV-2 coronavirus outbreak continues to spread at a rapid rate worldwide. The
main protease (Mpro) is an attractive target for anti-COVID-19 agents. Unexpected difficulties …

[PDF][PDF] Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2

BT Berger, M Amaral, DB Kokh, A Nunes-Alves… - Cell Chemical …, 2021 - cell.com
There is increasing evidence of a significant correlation between prolonged drug-target
residence time and increased drug efficacy. Here, we report a structural rationale for kinetic …