FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2078220227> ?p ?o ?g. }

• W2078220227 abstract "Optimization to identify the global minimum energy conformation sequence in in silico enzyme design is computationally non-deterministic polynomial-time (NP)-hard, with the search time growing exponentially as the number of design sites increases. This drawback forces the modeling of protein-ligand systems to adopt discrete amino acid rotamers and ligand conformers, as well as continuum solvent treatment of the environment; however, such compromises produce large numbers of false positives in sequence selection. In this report, cephalosporin acylase, which catalyzes the hydrolytic reaction of cephalosporin C to 7-aminocephalosporanic acid, was used to investigate the dynamic features of active-site-transition-state complex structures using molecular dynamics (MD) simulations to potentially eliminate false positives. The molecular docking between cephalosporin C and wild type acylase N176 and its eight mutants showed that the rate-limiting step in the hydrolytic reaction of cephalosporin C is the acylation process. MD simulations of the active-site-transition-state complex structures of the acylation processes for N176 and its eight mutants showed that the geometrical constraints between catalytic residues and small molecule transition states are always well maintained during the 20 ns simulation for mutants with higher activities, and more hydrogen bonds between binding residues and functional groups of the ligand side chain in the active pocket are formed for mutants with higher activities. The conformations of the ligand transition states were changed greatly after the simulation. This indicates that the hydrogen bond network between the ligand and protein could be improved to enhance the activity of cephalosporin C acylase in subsequent design." @default.
• W2078220227 created "2016-06-24" @default.
• W2078220227 creator A5008367015 @default.
• W2078220227 creator A5053780153 @default.
• W2078220227 creator A5072178740 @default.
• W2078220227 date "2014-06-17" @default.
• W2078220227 modified "2023-10-14" @default.
• W2078220227 title "Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking" @default.
• W2078220227 cites W1975338077 @default.
• W2078220227 cites W1984021058 @default.
• W2078220227 cites W1984180361 @default.
• W2078220227 cites W1987696643 @default.
• W2078220227 cites W1989686471 @default.
• W2078220227 cites W1992904904 @default.
• W2078220227 cites W2002219567 @default.
• W2078220227 cites W2035687084 @default.
• W2078220227 cites W2044430464 @default.
• W2078220227 cites W2055276124 @default.
• W2078220227 cites W2056183134 @default.
• W2078220227 cites W2057477511 @default.
• W2078220227 cites W2063684507 @default.
• W2078220227 cites W2066381187 @default.
• W2078220227 cites W2067174909 @default.
• W2078220227 cites W2071566170 @default.
• W2078220227 cites W2073302350 @default.
• W2078220227 cites W2081693079 @default.
• W2078220227 cites W2082260955 @default.
• W2078220227 cites W2090826418 @default.
• W2078220227 cites W2097985831 @default.
• W2078220227 cites W2114367386 @default.
• W2078220227 cites W2115580390 @default.
• W2078220227 cites W2115949736 @default.
• W2078220227 cites W2122976061 @default.
• W2078220227 cites W2128572087 @default.
• W2078220227 cites W2131003275 @default.
• W2078220227 cites W2146341417 @default.
• W2078220227 cites W2147304506 @default.
• W2078220227 cites W2153612149 @default.
• W2078220227 cites W2155636968 @default.
• W2078220227 cites W2160544821 @default.
• W2078220227 cites W2334047574 @default.
• W2078220227 doi "https://doi.org/10.1007/s00894-014-2314-5" @default.
• W2078220227 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24935111" @default.
• W2078220227 hasPublicationYear "2014" @default.
• W2078220227 type Work @default.
• W2078220227 sameAs 2078220227 @default.
• W2078220227 citedByCount "10" @default.
• W2078220227 countsByYear W20782202272016 @default.
• W2078220227 countsByYear W20782202272019 @default.
• W2078220227 countsByYear W20782202272020 @default.
• W2078220227 countsByYear W20782202272021 @default.
• W2078220227 crossrefType "journal-article" @default.
• W2078220227 hasAuthorship W2078220227A5008367015 @default.
• W2078220227 hasAuthorship W2078220227A5053780153 @default.
• W2078220227 hasAuthorship W2078220227A5072178740 @default.
• W2078220227 hasBestOaLocation W20782202272 @default.
• W2078220227 hasConcept C112887158 @default.
• W2078220227 hasConcept C116569031 @default.
• W2078220227 hasConcept C147597530 @default.
• W2078220227 hasConcept C159110408 @default.
• W2078220227 hasConcept C161790260 @default.
• W2078220227 hasConcept C170493617 @default.
• W2078220227 hasConcept C178790620 @default.
• W2078220227 hasConcept C181199279 @default.
• W2078220227 hasConcept C185592680 @default.
• W2078220227 hasConcept C18705241 @default.
• W2078220227 hasConcept C193557335 @default.
• W2078220227 hasConcept C2776067932 @default.
• W2078220227 hasConcept C32909587 @default.
• W2078220227 hasConcept C41183919 @default.
• W2078220227 hasConcept C41685203 @default.
• W2078220227 hasConcept C501593827 @default.
• W2078220227 hasConcept C55493867 @default.
• W2078220227 hasConcept C59593255 @default.
• W2078220227 hasConcept C64778159 @default.
• W2078220227 hasConcept C71240020 @default.
• W2078220227 hasConcept C71924100 @default.
• W2078220227 hasConcept C89031862 @default.
• W2078220227 hasConceptScore W2078220227C112887158 @default.
• W2078220227 hasConceptScore W2078220227C116569031 @default.
• W2078220227 hasConceptScore W2078220227C147597530 @default.
• W2078220227 hasConceptScore W2078220227C159110408 @default.
• W2078220227 hasConceptScore W2078220227C161790260 @default.
• W2078220227 hasConceptScore W2078220227C170493617 @default.
• W2078220227 hasConceptScore W2078220227C178790620 @default.
• W2078220227 hasConceptScore W2078220227C181199279 @default.
• W2078220227 hasConceptScore W2078220227C185592680 @default.
• W2078220227 hasConceptScore W2078220227C18705241 @default.
• W2078220227 hasConceptScore W2078220227C193557335 @default.
• W2078220227 hasConceptScore W2078220227C2776067932 @default.
• W2078220227 hasConceptScore W2078220227C32909587 @default.
• W2078220227 hasConceptScore W2078220227C41183919 @default.
• W2078220227 hasConceptScore W2078220227C41685203 @default.
• W2078220227 hasConceptScore W2078220227C501593827 @default.
• W2078220227 hasConceptScore W2078220227C55493867 @default.
• W2078220227 hasConceptScore W2078220227C59593255 @default.
• W2078220227 hasConceptScore W2078220227C64778159 @default.
• W2078220227 hasConceptScore W2078220227C71240020 @default.
• W2078220227 hasConceptScore W2078220227C71924100 @default.
• W2078220227 hasConceptScore W2078220227C89031862 @default.

• next