FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W1984563996> ?p ?o ?g. }

• W1984563996 endingPage "458" @default.
• W1984563996 startingPage "441" @default.
• W1984563996 abstract "Depth is a term frequently applied to the shape and surface of macromolecules, describing for example the grooves in DNA, the shape of an enzyme active site, or the binding site for a small molecule in a protein. Yet depth is a difficult property to define rigorously in a macromolecule, and few computational tools exist to quantify this notion, to visualize it, or analyze the results. We present our notion of travel depth, simply put the physical distance a solvent molecule would have to travel from a surface point to a suitably defined reference surface. To define the reference surface, we use the limiting form of the molecular surface with increasing probe size: the convex hull. We then present a fast, robust approximation algorithm to compute travel depth to every surface point. The travel depth is useful because it works for pockets of any size and complexity. It also works for two interesting special cases. First, it works on the grooves in DNA, which are unbounded in one direction. Second, it works on the case of tunnels, that is pockets that have no “bottom”, but go through the entire macromolecule. Our algorithm makes it straightforward to quantify discussions of depth when analyzing structures. High-throughput analysis of macromolecule depth is also enabled by our algorithm. This is demonstrated by analyzing a database of protein-small molecule binding pockets, and the distribution of bound magnesium ions in RNA structures. These analyses show significant, but subtle effects of depth on ligand binding localization and strength." @default.
• W1984563996 created "2016-06-24" @default.
• W1984563996 creator A5059008811 @default.
• W1984563996 creator A5080493709 @default.
• W1984563996 date "2006-09-01" @default.
• W1984563996 modified "2023-10-17" @default.
• W1984563996 title "Travel Depth, a New Shape Descriptor for Macromolecules: Application to Ligand Binding" @default.
• W1984563996 cites W1576626155 @default.
• W1984563996 cites W1963836754 @default.
• W1984563996 cites W1967724786 @default.
• W1984563996 cites W1973503110 @default.
• W1984563996 cites W1993046136 @default.
• W1984563996 cites W2005653514 @default.
• W1984563996 cites W2022211160 @default.
• W1984563996 cites W2023219682 @default.
• W1984563996 cites W2030841140 @default.
• W1984563996 cites W2030860488 @default.
• W1984563996 cites W2032029058 @default.
• W1984563996 cites W2035954399 @default.
• W1984563996 cites W2043901383 @default.
• W1984563996 cites W2043995349 @default.
• W1984563996 cites W2067009594 @default.
• W1984563996 cites W2090774487 @default.
• W1984563996 cites W2091563009 @default.
• W1984563996 cites W2092285329 @default.
• W1984563996 cites W2092638542 @default.
• W1984563996 cites W2101532349 @default.
• W1984563996 cites W2105902442 @default.
• W1984563996 cites W2106315897 @default.
• W1984563996 cites W2108508060 @default.
• W1984563996 cites W2117744495 @default.
• W1984563996 cites W2127073449 @default.
• W1984563996 cites W2130479394 @default.
• W1984563996 cites W2140407975 @default.
• W1984563996 cites W2144714500 @default.
• W1984563996 cites W2163178194 @default.
• W1984563996 cites W2165181282 @default.
• W1984563996 cites W2177655263 @default.
• W1984563996 cites W2177731497 @default.
• W1984563996 cites W2330973325 @default.
• W1984563996 cites W2333297418 @default.
• W1984563996 cites W3139495523 @default.
• W1984563996 doi "https://doi.org/10.1016/j.jmb.2006.07.022" @default.
• W1984563996 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16934837" @default.
• W1984563996 hasPublicationYear "2006" @default.
• W1984563996 type Work @default.
• W1984563996 sameAs 1984563996 @default.
• W1984563996 citedByCount "82" @default.
• W1984563996 countsByYear W19845639962012 @default.
• W1984563996 countsByYear W19845639962013 @default.
• W1984563996 countsByYear W19845639962014 @default.
• W1984563996 countsByYear W19845639962015 @default.
• W1984563996 countsByYear W19845639962016 @default.
• W1984563996 countsByYear W19845639962017 @default.
• W1984563996 countsByYear W19845639962019 @default.
• W1984563996 countsByYear W19845639962020 @default.
• W1984563996 countsByYear W19845639962021 @default.
• W1984563996 countsByYear W19845639962023 @default.
• W1984563996 crossrefType "journal-article" @default.
• W1984563996 hasAuthorship W1984563996A5059008811 @default.
• W1984563996 hasAuthorship W1984563996A5080493709 @default.
• W1984563996 hasConcept C112680207 @default.
• W1984563996 hasConcept C11413529 @default.
• W1984563996 hasConcept C116569031 @default.
• W1984563996 hasConcept C159467904 @default.
• W1984563996 hasConcept C170493617 @default.
• W1984563996 hasConcept C178790620 @default.
• W1984563996 hasConcept C185592680 @default.
• W1984563996 hasConcept C186060115 @default.
• W1984563996 hasConcept C204389451 @default.
• W1984563996 hasConcept C2524010 @default.
• W1984563996 hasConcept C2776799497 @default.
• W1984563996 hasConcept C28719098 @default.
• W1984563996 hasConcept C32909587 @default.
• W1984563996 hasConcept C33923547 @default.
• W1984563996 hasConcept C41008148 @default.
• W1984563996 hasConcept C55493867 @default.
• W1984563996 hasConcept C86803240 @default.
• W1984563996 hasConceptScore W1984563996C112680207 @default.
• W1984563996 hasConceptScore W1984563996C11413529 @default.
• W1984563996 hasConceptScore W1984563996C116569031 @default.
• W1984563996 hasConceptScore W1984563996C159467904 @default.
• W1984563996 hasConceptScore W1984563996C170493617 @default.
• W1984563996 hasConceptScore W1984563996C178790620 @default.
• W1984563996 hasConceptScore W1984563996C185592680 @default.
• W1984563996 hasConceptScore W1984563996C186060115 @default.
• W1984563996 hasConceptScore W1984563996C204389451 @default.
• W1984563996 hasConceptScore W1984563996C2524010 @default.
• W1984563996 hasConceptScore W1984563996C2776799497 @default.
• W1984563996 hasConceptScore W1984563996C28719098 @default.
• W1984563996 hasConceptScore W1984563996C32909587 @default.
• W1984563996 hasConceptScore W1984563996C33923547 @default.
• W1984563996 hasConceptScore W1984563996C41008148 @default.
• W1984563996 hasConceptScore W1984563996C55493867 @default.
• W1984563996 hasConceptScore W1984563996C86803240 @default.
• W1984563996 hasIssue "3" @default.
• W1984563996 hasLocation W19845639961 @default.
• W1984563996 hasLocation W19845639962 @default.

• next