Matches in SemOpenAlex for { <https://semopenalex.org/work/W3004719370> ?p ?o ?g. }
Showing items 1 to 78 of
78
with 100 items per page.
- W3004719370 endingPage "141a" @default.
- W3004719370 startingPage "141a" @default.
- W3004719370 abstract "Many proteins, regardless of their function, can be regulated by a myriad of small molecules. Knowing the details of these interactions in molecular scale is a key point to understand the mechanism of biological processes. However, protein modulation by small ligands have complex features: there may exist multiple binding sites, with different occupancy states, many ligand configurations and varying affinities. A good description of these phenomena can be obtained by flooding Molecular Dynamics (flooding-MD), which is a simulation with a complete protein system added a fixed number of ligands. Usually, the main information obtained are high-probability ligand regions nearby the receptor. However, truthful results require long computational timescales due to convergence of a huge number of states. Given the effort put into these simulations, here we present an optimized framework to analyze flooding-MD simulations, capable of reconstructing ligand binding constants, which will be able to describe several interaction properties in any desired concentration - occupancy probabilities, spatial probabilities, mean bound ligand numbers and site affinities - without the need to run new simulations. We illustrate the use of the framework for the mammalian voltage-gated potassium channel Kv1.2, and sevoflurane, a positive modulator. For each concentration ranging from 50mM to 150mM sevoflurane, >200ns flooding-MD simulations were performed. From the highest concentrated simulation (150mM), for each site, the theory was applied to estimate the binding constants and other properties at more diluted concentrations. In order to verify accuracy of these projections, they were directly compared to more diluted flooding-MD simulations (<150mM sevoflurane) properties and had satisfying results, within an error margin. This improved way of analyzing flooding-MDs can be applied to diverse protein-ligand interactions, offering a simpler and faster way to study these interactions, without the need of additional simulations." @default.
- W3004719370 created "2020-02-14" @default.
- W3004719370 creator A5016781804 @default.
- W3004719370 creator A5032070347 @default.
- W3004719370 creator A5061322530 @default.
- W3004719370 date "2020-02-01" @default.
- W3004719370 modified "2023-10-15" @default.
- W3004719370 title "Improved Flooding Molecular Dynamics Analysis" @default.
- W3004719370 doi "https://doi.org/10.1016/j.bpj.2019.11.896" @default.
- W3004719370 hasPublicationYear "2020" @default.
- W3004719370 type Work @default.
- W3004719370 sameAs 3004719370 @default.
- W3004719370 citedByCount "1" @default.
- W3004719370 countsByYear W30047193702023 @default.
- W3004719370 crossrefType "journal-article" @default.
- W3004719370 hasAuthorship W3004719370A5016781804 @default.
- W3004719370 hasAuthorship W3004719370A5032070347 @default.
- W3004719370 hasAuthorship W3004719370A5061322530 @default.
- W3004719370 hasBestOaLocation W30047193701 @default.
- W3004719370 hasConcept C116569031 @default.
- W3004719370 hasConcept C121332964 @default.
- W3004719370 hasConcept C121864883 @default.
- W3004719370 hasConcept C147597530 @default.
- W3004719370 hasConcept C15744967 @default.
- W3004719370 hasConcept C162324750 @default.
- W3004719370 hasConcept C170493617 @default.
- W3004719370 hasConcept C185592680 @default.
- W3004719370 hasConcept C186060115 @default.
- W3004719370 hasConcept C186594467 @default.
- W3004719370 hasConcept C2777303404 @default.
- W3004719370 hasConcept C2780283098 @default.
- W3004719370 hasConcept C41008148 @default.
- W3004719370 hasConcept C50522688 @default.
- W3004719370 hasConcept C542102704 @default.
- W3004719370 hasConcept C55493867 @default.
- W3004719370 hasConcept C59593255 @default.
- W3004719370 hasConcept C71240020 @default.
- W3004719370 hasConcept C86803240 @default.
- W3004719370 hasConceptScore W3004719370C116569031 @default.
- W3004719370 hasConceptScore W3004719370C121332964 @default.
- W3004719370 hasConceptScore W3004719370C121864883 @default.
- W3004719370 hasConceptScore W3004719370C147597530 @default.
- W3004719370 hasConceptScore W3004719370C15744967 @default.
- W3004719370 hasConceptScore W3004719370C162324750 @default.
- W3004719370 hasConceptScore W3004719370C170493617 @default.
- W3004719370 hasConceptScore W3004719370C185592680 @default.
- W3004719370 hasConceptScore W3004719370C186060115 @default.
- W3004719370 hasConceptScore W3004719370C186594467 @default.
- W3004719370 hasConceptScore W3004719370C2777303404 @default.
- W3004719370 hasConceptScore W3004719370C2780283098 @default.
- W3004719370 hasConceptScore W3004719370C41008148 @default.
- W3004719370 hasConceptScore W3004719370C50522688 @default.
- W3004719370 hasConceptScore W3004719370C542102704 @default.
- W3004719370 hasConceptScore W3004719370C55493867 @default.
- W3004719370 hasConceptScore W3004719370C59593255 @default.
- W3004719370 hasConceptScore W3004719370C71240020 @default.
- W3004719370 hasConceptScore W3004719370C86803240 @default.
- W3004719370 hasIssue "3" @default.
- W3004719370 hasLocation W30047193701 @default.
- W3004719370 hasOpenAccess W3004719370 @default.
- W3004719370 hasPrimaryLocation W30047193701 @default.
- W3004719370 hasRelatedWork W1971291106 @default.
- W3004719370 hasRelatedWork W1974414168 @default.
- W3004719370 hasRelatedWork W1996889227 @default.
- W3004719370 hasRelatedWork W2120642597 @default.
- W3004719370 hasRelatedWork W2123691719 @default.
- W3004719370 hasRelatedWork W2337206335 @default.
- W3004719370 hasRelatedWork W2924053807 @default.
- W3004719370 hasRelatedWork W3016068439 @default.
- W3004719370 hasRelatedWork W4241081643 @default.
- W3004719370 hasRelatedWork W2769641421 @default.
- W3004719370 hasVolume "118" @default.
- W3004719370 isParatext "false" @default.
- W3004719370 isRetracted "false" @default.
- W3004719370 magId "3004719370" @default.
- W3004719370 workType "article" @default.