FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2061750520> ?p ?o ?g. }

• W2061750520 endingPage "325" @default.
• W2061750520 startingPage "311" @default.
• W2061750520 abstract "Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded a previously used diverse “cross-docking” benchmark to thirty ligand–protein pairs extracted from different crystal structures. The algorithm systematically scans pairs of neighbouring side chains, replaces them by alanines, and docks the ligand to each ‘gapped’ version of the pocket. All docked positions are scored, refined with original side chains and flexible backbone and re-scored. In the optimal version of the protocol pairs of residues were replaced by alanines and only one best scoring conformation was selected from each ‘gapped’ pocket for refinement. The optimal SCARE (SCan Alanines and REfine) protocol identifies a near native conformation (under 2 Å RMSD) as the lowest rank for 80% of pairs if the docking bounding box is defined by the predicted pocket envelope, and for as many as 90% of the pairs if the bounding box is derived from the known answer with ∼5 Å margin as used in most previous publications. The presented fully automated algorithm takes about 2 h per pose of a single processor time, requires only one pocket structure and no prior knowledge about the binding site location. Furthermore, the results for conformationally conserved pockets do not deteriorate due to substantial increase of the pocket variability." @default.
• W2061750520 created "2016-06-24" @default.
• W2061750520 creator A5004550798 @default.
• W2061750520 creator A5064101943 @default.
• W2061750520 creator A5070322806 @default.
• W2061750520 creator A5076090370 @default.
• W2061750520 date "2008-02-14" @default.
• W2061750520 modified "2023-10-11" @default.
• W2061750520 title "A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)" @default.
• W2061750520 cites W1574312817 @default.
• W2061750520 cites W1969875513 @default.
• W2061750520 cites W1974422922 @default.
• W2061750520 cites W1974645077 @default.
• W2061750520 cites W1974977468 @default.
• W2061750520 cites W1975691556 @default.
• W2061750520 cites W1983194490 @default.
• W2061750520 cites W1986240377 @default.
• W2061750520 cites W1990137109 @default.
• W2061750520 cites W1995186828 @default.
• W2061750520 cites W2003127541 @default.
• W2061750520 cites W2019732485 @default.
• W2061750520 cites W2023940675 @default.
• W2061750520 cites W2027638447 @default.
• W2061750520 cites W2034126246 @default.
• W2061750520 cites W2057846043 @default.
• W2061750520 cites W2062378498 @default.
• W2061750520 cites W2066143642 @default.
• W2061750520 cites W2069982778 @default.
• W2061750520 cites W2072180710 @default.
• W2061750520 cites W2072351846 @default.
• W2061750520 cites W2084375915 @default.
• W2061750520 cites W2091734240 @default.
• W2061750520 cites W2097612485 @default.
• W2061750520 cites W2103994532 @default.
• W2061750520 cites W2123028643 @default.
• W2061750520 cites W2136640191 @default.
• W2061750520 cites W2149289547 @default.
• W2061750520 cites W2160188189 @default.
• W2061750520 cites W2167041509 @default.
• W2061750520 cites W4296588184 @default.
• W2061750520 doi "https://doi.org/10.1007/s10822-008-9188-5" @default.
• W2061750520 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2641994" @default.
• W2061750520 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/18273556" @default.
• W2061750520 hasPublicationYear "2008" @default.
• W2061750520 type Work @default.
• W2061750520 sameAs 2061750520 @default.
• W2061750520 citedByCount "76" @default.
• W2061750520 countsByYear W20617505202012 @default.
• W2061750520 countsByYear W20617505202013 @default.
• W2061750520 countsByYear W20617505202014 @default.
• W2061750520 countsByYear W20617505202015 @default.
• W2061750520 countsByYear W20617505202016 @default.
• W2061750520 countsByYear W20617505202017 @default.
• W2061750520 countsByYear W20617505202018 @default.
• W2061750520 countsByYear W20617505202019 @default.
• W2061750520 countsByYear W20617505202020 @default.
• W2061750520 countsByYear W20617505202021 @default.
• W2061750520 countsByYear W20617505202022 @default.
• W2061750520 countsByYear W20617505202023 @default.
• W2061750520 crossrefType "journal-article" @default.
• W2061750520 hasAuthorship W2061750520A5004550798 @default.
• W2061750520 hasAuthorship W2061750520A5064101943 @default.
• W2061750520 hasAuthorship W2061750520A5070322806 @default.
• W2061750520 hasAuthorship W2061750520A5076090370 @default.
• W2061750520 hasBestOaLocation W20617505202 @default.
• W2061750520 hasConcept C104317684 @default.
• W2061750520 hasConcept C115961682 @default.
• W2061750520 hasConcept C116569031 @default.
• W2061750520 hasConcept C147037132 @default.
• W2061750520 hasConcept C154945302 @default.
• W2061750520 hasConcept C159110408 @default.
• W2061750520 hasConcept C16318435 @default.
• W2061750520 hasConcept C170493617 @default.
• W2061750520 hasConcept C185592680 @default.
• W2061750520 hasConcept C2780227090 @default.
• W2061750520 hasConcept C41008148 @default.
• W2061750520 hasConcept C41685203 @default.
• W2061750520 hasConcept C501734568 @default.
• W2061750520 hasConcept C55493867 @default.
• W2061750520 hasConcept C71240020 @default.
• W2061750520 hasConcept C71924100 @default.
• W2061750520 hasConcept C8010536 @default.
• W2061750520 hasConceptScore W2061750520C104317684 @default.
• W2061750520 hasConceptScore W2061750520C115961682 @default.
• W2061750520 hasConceptScore W2061750520C116569031 @default.
• W2061750520 hasConceptScore W2061750520C147037132 @default.
• W2061750520 hasConceptScore W2061750520C154945302 @default.
• W2061750520 hasConceptScore W2061750520C159110408 @default.
• W2061750520 hasConceptScore W2061750520C16318435 @default.
• W2061750520 hasConceptScore W2061750520C170493617 @default.
• W2061750520 hasConceptScore W2061750520C185592680 @default.
• W2061750520 hasConceptScore W2061750520C2780227090 @default.
• W2061750520 hasConceptScore W2061750520C41008148 @default.
• W2061750520 hasConceptScore W2061750520C41685203 @default.
• W2061750520 hasConceptScore W2061750520C501734568 @default.
• W2061750520 hasConceptScore W2061750520C55493867 @default.
• W2061750520 hasConceptScore W2061750520C71240020 @default.
• W2061750520 hasConceptScore W2061750520C71924100 @default.

• next