Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Conference object . 2022
License: CC BY
Data sources: Datacite
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Other literature type . 2022
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Conference object . 2022
License: CC BY
Data sources: Datacite
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
versions View all 3 versions
addClaim

Investigation of the Orthogonal Degrees of Freedom in Protein-Drug Unbinding Pathways of the ABL Protein Using Replica Exchange Transition Interface Sampling

Authors: Vervust, Wouter; Ghysels, An;

Investigation of the Orthogonal Degrees of Freedom in Protein-Drug Unbinding Pathways of the ABL Protein Using Replica Exchange Transition Interface Sampling

Abstract

Both thermodynamic selectivity and kinetic selectivity are important determinants for the in vivo efficacy of candidate drug molecules. Computational tools to predict thermodynamic and kinetic parameters are therefore necessary for the screening stage of the drug-design pipeline. As the timescale of most drug (un)binding processes is out of reach for conventional molecular dynamics simulations, specialized methodologies are needed to determine the (un)binding rates and residence times of protein-drug complexes. To assess the kinetics, most methods require the definition of a reaction coordinate that accurately describes the progression of the (un)binding process. As these (un)binding pathways are not known a priori, it is possible that free energy barriers are hidden along degrees of freedom (DoFs) that are orthogonal to the low-dimensional and user-defined reaction coordinate, resulting in inaccurate kinetics. In this study, Replica Exchange Transition Interface Sampling (RETIS) [1] is used to investigate the orthogonal DoFs in the unbinding pathways of imatinib to the kinase protein ABL (wild type and mutated variants). RETIS is an exact path sampling method, which generates trajectories using shooting moves, and which accepts or rejects trajectories using a Monte Carlo algorithm. RETIS is reaction-coordinate independent and produces reactive trajectories as if they originated from a long molecular dynamics simulation. As such, the hidden energy barriers should be captured by the paths generated by RETIS, which will be presented here. Reference [1] R. Cabriolu, K. M. Skjelbred Refsnes, P. G. Bolhuis, and T. S. Van Erp, “Foundations and latest advances in replica exchange transition interface sampling,” J. Chem. Phys., vol. 147, no. 15, 2017.

Country
Belgium
Related Organizations
Keywords

Technology and Engineering

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
    OpenAIRE UsageCounts
    Usage byUsageCounts
    visibility views 2
    download downloads 5
  • 2
    views
    5
    downloads
    Powered byOpenAIRE UsageCounts
Powered by OpenAIRE graph
Found an issue? Give us feedback
visibility
download
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
views
OpenAIRE UsageCountsViews provided by UsageCounts
downloads
OpenAIRE UsageCountsDownloads provided by UsageCounts
0
Average
Average
Average
2
5
Green