FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W1036232568> ?p ?o ?g. }

• W1036232568 endingPage "84" @default.
• W1036232568 startingPage "78" @default.
• W1036232568 abstract "Protein-carbohydrate interactions (PCIs) involve a variety of essential biological processes such as cell recognition and migration, metabolism processes and immunological reactions, which are important for securing functions of living organisms. Due to the polysaccharide structural diversity and dynamics flexibility, PCIs can be very difficult for experimental measurement and computer prediction. Here we report a simple method for docking polysaccharide to proteins whose binding pockets have a Tryptophan box. The method samples polysaccharide conformations using constraint conditions imposed by the box, evaluate the conformation energies based on a knowledge-based potential function, and finds the best docking structures using the conventional Monte Carlo simulated annealing technique. We applied the method to dock polysaccharides with 2 to 4 monomers to three carbohydrate-binding proteins, whose pockets have clear aromatic residue-defined binding channels. The predictions found correct carbohydrate binding conformations with atomic RMSD of 1.1-1.6 Å from X-ray crystal structures. The calculation can be performed in ordinary PC and only cost a couple of minutes for a single docking. Our method, when combined with other docking programs, provides a reliable start conformation for further accurate simulation of PCIs." @default.
• W1036232568 created "2016-06-24" @default.
• W1036232568 creator A5005618066 @default.
• W1036232568 creator A5008144578 @default.
• W1036232568 creator A5060691203 @default.
• W1036232568 date "2015-09-01" @default.
• W1036232568 modified "2023-10-08" @default.
• W1036232568 title "Docking polysaccharide to proteins that have a Tryptophan box in the binding pocket" @default.
• W1036232568 cites W1977379770 @default.
• W1036232568 cites W1981069567 @default.
• W1036232568 cites W1987433783 @default.
• W1036232568 cites W1988966516 @default.
• W1036232568 cites W1990011877 @default.
• W1036232568 cites W1995513207 @default.
• W1036232568 cites W1995601054 @default.
• W1036232568 cites W2018834778 @default.
• W1036232568 cites W2020421862 @default.
• W1036232568 cites W2021268536 @default.
• W1036232568 cites W2024060531 @default.
• W1036232568 cites W2027408247 @default.
• W1036232568 cites W2033268106 @default.
• W1036232568 cites W2050595677 @default.
• W1036232568 cites W2060577276 @default.
• W1036232568 cites W2070457843 @default.
• W1036232568 cites W2071466250 @default.
• W1036232568 cites W2072197675 @default.
• W1036232568 cites W2077456478 @default.
• W1036232568 cites W2078516832 @default.
• W1036232568 cites W2082030984 @default.
• W1036232568 cites W2084891561 @default.
• W1036232568 cites W2085259430 @default.
• W1036232568 cites W2086088308 @default.
• W1036232568 cites W2094235329 @default.
• W1036232568 cites W2095022339 @default.
• W1036232568 cites W2108929776 @default.
• W1036232568 cites W2109937808 @default.
• W1036232568 cites W2111677828 @default.
• W1036232568 cites W2118016981 @default.
• W1036232568 cites W2118672858 @default.
• W1036232568 cites W2118673710 @default.
• W1036232568 cites W2130479394 @default.
• W1036232568 cites W2149170824 @default.
• W1036232568 cites W2154061444 @default.
• W1036232568 cites W2168020978 @default.
• W1036232568 cites W2171677744 @default.
• W1036232568 cites W2314331064 @default.
• W1036232568 cites W2336022154 @default.
• W1036232568 cites W2401162373 @default.
• W1036232568 doi "https://doi.org/10.1016/j.carres.2015.07.013" @default.
• W1036232568 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26257378" @default.
• W1036232568 hasPublicationYear "2015" @default.
• W1036232568 type Work @default.
• W1036232568 sameAs 1036232568 @default.
• W1036232568 citedByCount "5" @default.
• W1036232568 countsByYear W10362325682018 @default.
• W1036232568 countsByYear W10362325682019 @default.
• W1036232568 countsByYear W10362325682020 @default.
• W1036232568 countsByYear W10362325682022 @default.
• W1036232568 crossrefType "journal-article" @default.
• W1036232568 hasAuthorship W1036232568A5005618066 @default.
• W1036232568 hasAuthorship W1036232568A5008144578 @default.
• W1036232568 hasAuthorship W1036232568A5060691203 @default.
• W1036232568 hasConcept C100817775 @default.
• W1036232568 hasConcept C11413529 @default.
• W1036232568 hasConcept C126980161 @default.
• W1036232568 hasConcept C159110408 @default.
• W1036232568 hasConcept C185592680 @default.
• W1036232568 hasConcept C186060115 @default.
• W1036232568 hasConcept C204389451 @default.
• W1036232568 hasConcept C2776706248 @default.
• W1036232568 hasConcept C41008148 @default.
• W1036232568 hasConcept C41685203 @default.
• W1036232568 hasConcept C44695244 @default.
• W1036232568 hasConcept C47701112 @default.
• W1036232568 hasConcept C515207424 @default.
• W1036232568 hasConcept C55493867 @default.
• W1036232568 hasConcept C70721500 @default.
• W1036232568 hasConcept C71240020 @default.
• W1036232568 hasConcept C71924100 @default.
• W1036232568 hasConcept C8010536 @default.
• W1036232568 hasConcept C86803240 @default.
• W1036232568 hasConceptScore W1036232568C100817775 @default.
• W1036232568 hasConceptScore W1036232568C11413529 @default.
• W1036232568 hasConceptScore W1036232568C126980161 @default.
• W1036232568 hasConceptScore W1036232568C159110408 @default.
• W1036232568 hasConceptScore W1036232568C185592680 @default.
• W1036232568 hasConceptScore W1036232568C186060115 @default.
• W1036232568 hasConceptScore W1036232568C204389451 @default.
• W1036232568 hasConceptScore W1036232568C2776706248 @default.
• W1036232568 hasConceptScore W1036232568C41008148 @default.
• W1036232568 hasConceptScore W1036232568C41685203 @default.
• W1036232568 hasConceptScore W1036232568C44695244 @default.
• W1036232568 hasConceptScore W1036232568C47701112 @default.
• W1036232568 hasConceptScore W1036232568C515207424 @default.
• W1036232568 hasConceptScore W1036232568C55493867 @default.
• W1036232568 hasConceptScore W1036232568C70721500 @default.
• W1036232568 hasConceptScore W1036232568C71240020 @default.
• W1036232568 hasConceptScore W1036232568C71924100 @default.

• next