ArticleJournal of chemical theory and computation2011
Insights into Ligand-Protein Binding from Local Mechanical Response.
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- On Free Energy Calculations in Drug Discovery.Accounts of chemical research · 2025Article
- Metadynamics-Based Approaches for Modeling the Hypoxia-Inducible Factor 2α Ligand Binding Process.Journal of chemical theory and computation · 2021Article
- In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome.European biophysics journal : EBJ · 2017Article
- Extracting ligands from receptors by reversed targeted molecular dynamics.Journal of computer-aided molecular design · 2015Article
- Why nature really chose phosphate.Quarterly reviews of biophysics · 2013Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational studies of ligand-protein binding are crucial for properly designing novel compounds of potential pharmacological interest. In this respect, researchers are increasingly interested in steered molecular dynamics for ligand-protein binding and unbinding studies. In particular, it has been suggested that analyzing the work profiles along the ligand-protein undocking paths could be fruitful. Here, we propose that small portions of work profiles, termed "local mechanical responses" of the system to a steering force, could serve as a universal measure for capturing relevant information about the system under investigation. Specifically, we first collected a high number of steering trajectories using two biological systems of increasing complexity (i.e., alanine dipeptide and (R)-roscovitine/CDK5 complex). Then, we devised a novel postprocessing tool to be applied to the local mechanical responses, to extract structural information related to the biological processes under investigation. Despite the out-of-equilibrium character of the trajectories, the analysis carried out on the work profiles provided pivotal information about the investigated biological processes. This could eventually be applied to drug design.
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Registered trials
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