User profiles for Daria B. Kokh
Daria B. KokhCancer Registry of Baden-Württemberg Verified email at klr-krbw.de Cited by 3116 |
Protein binding pocket dynamics
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 …
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 …
challenging to predict computationally and, therefore, is usually not considered in the early …
Modeling and simulation of protein–surface interactions: achievements and challenges
Understanding protein–inorganic surface interactions is central to the rational design of new
tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant …
tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant …
Kinetics for Drug Discovery: an industry-driven effort to target drug residence time
… 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 …
(b) Different strategies required for improvement of K D , k on and k off values (yellow, orange …
Docking of ubiquitin to gold nanoparticles
Protein–nanoparticle associations have important applications in nanoscience and
nanotechnology such as targeted drug delivery and theranostics. However, the mechanisms by …
nanotechnology such as targeted drug delivery and theranostics. However, the mechanisms by …
New approaches for computing ligand–receptor binding kinetics
… 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… N-terminal domain of HSP90 and of focal adhesion kinase (Kokh et al., unpublished data). …
… N-terminal domain of HSP90 and of focal adhesion kinase (Kokh et al., unpublished data).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 …
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 …
range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far …
Recent progress in molecular simulation methods for drug binding kinetics
… 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-…
… (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
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 …
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
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 …
residence time and increased drug efficacy. Here, we report a structural rationale for kinetic …