FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2028343389> ?p ?o ?g. }

• W2028343389 endingPage "2666" @default.
• W2028343389 startingPage "2656" @default.
• W2028343389 abstract "We performed a detailed analysis of conformational transition pathways for a set of 10 proteins, which undergo large hinge-bending-type motions with 4–12 Å RMSD (root mean-square distance) between open and closed crystal structures. Anisotropic network model-Monte Carlo (ANM-MC) algorithm generates a targeted pathway between two conformations, where the collective modes from the ANM are used for deformation at each iteration and the conformational energy of the deformed structure is minimized via an MC algorithm. The target structure was approached successfully with an RMSD of 0.9–4.1 Å when a relatively low cutoff radius of 10 Å was used in ANM. Even though one predominant mode (first or second) directed the open-to-closed conformational transition, changes in the dominant mode character were observed for most cases along the transition. By imposing radius of gyration constraint during mode selection, it was possible to predict the closed structure for eight out of 10 proteins (with initial 4.1–7.1 Å and final 1.7–2.9 Å RMSD to target). Deforming along a single mode leads to most successful predictions. Based on the previously reported free energy surface of adenylate kinase, deformations along the first mode produced an energetically favorable path, which was interestingly facilitated by a change in mode shape (resembling second and third modes) at key points. Pathway intermediates are provided in our database of conformational transitions (http://safir.prc.boun.edu.tr/anmmc/method/1)." @default.
• W2028343389 created "2016-06-24" @default.
• W2028343389 creator A5020239421 @default.
• W2028343389 creator A5038256975 @default.
• W2028343389 creator A5072762331 @default.
• W2028343389 creator A5080732397 @default.
• W2028343389 date "2014-06-01" @default.
• W2028343389 modified "2023-10-17" @default.
• W2028343389 title "Features of Large Hinge-Bending Conformational Transitions. Prediction of Closed Structure from Open State" @default.
• W2028343389 cites W1969548780 @default.
• W2028343389 cites W1970454429 @default.
• W2028343389 cites W1975292161 @default.
• W2028343389 cites W1980430311 @default.
• W2028343389 cites W1988214145 @default.
• W2028343389 cites W1989161865 @default.
• W2028343389 cites W1990238127 @default.
• W2028343389 cites W1994059052 @default.
• W2028343389 cites W1997486650 @default.
• W2028343389 cites W2000690605 @default.
• W2028343389 cites W2004067483 @default.
• W2028343389 cites W2014425795 @default.
• W2028343389 cites W2020446183 @default.
• W2028343389 cites W2028603499 @default.
• W2028343389 cites W2031340110 @default.
• W2028343389 cites W2031822741 @default.
• W2028343389 cites W2045196944 @default.
• W2028343389 cites W2046221312 @default.
• W2028343389 cites W2051893115 @default.
• W2028343389 cites W2055141456 @default.
• W2028343389 cites W2056637556 @default.
• W2028343389 cites W2057594534 @default.
• W2028343389 cites W2059928115 @default.
• W2028343389 cites W2062809320 @default.
• W2028343389 cites W2067763399 @default.
• W2028343389 cites W2075769790 @default.
• W2028343389 cites W2076488922 @default.
• W2028343389 cites W2082028745 @default.
• W2028343389 cites W2085277871 @default.
• W2028343389 cites W2097294533 @default.
• W2028343389 cites W2103717543 @default.
• W2028343389 cites W2103856741 @default.
• W2028343389 cites W2113971181 @default.
• W2028343389 cites W2113994268 @default.
• W2028343389 cites W2118733486 @default.
• W2028343389 cites W2124483575 @default.
• W2028343389 cites W2129931931 @default.
• W2028343389 cites W2140889378 @default.
• W2028343389 cites W2142872962 @default.
• W2028343389 cites W2158726511 @default.
• W2028343389 cites W2168481503 @default.
• W2028343389 cites W2274240652 @default.
• W2028343389 cites W4299592781 @default.
• W2028343389 cites W4321317585 @default.
• W2028343389 doi "https://doi.org/10.1016/j.bpj.2014.05.017" @default.
• W2028343389 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4070069" @default.
• W2028343389 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24940783" @default.
• W2028343389 hasPublicationYear "2014" @default.
• W2028343389 type Work @default.
• W2028343389 sameAs 2028343389 @default.
• W2028343389 citedByCount "20" @default.
• W2028343389 countsByYear W20283433892015 @default.
• W2028343389 countsByYear W20283433892016 @default.
• W2028343389 countsByYear W20283433892017 @default.
• W2028343389 countsByYear W20283433892018 @default.
• W2028343389 countsByYear W20283433892019 @default.
• W2028343389 countsByYear W20283433892020 @default.
• W2028343389 countsByYear W20283433892021 @default.
• W2028343389 countsByYear W20283433892022 @default.
• W2028343389 countsByYear W20283433892023 @default.
• W2028343389 crossrefType "journal-article" @default.
• W2028343389 hasAuthorship W2028343389A5020239421 @default.
• W2028343389 hasAuthorship W2028343389A5038256975 @default.
• W2028343389 hasAuthorship W2028343389A5072762331 @default.
• W2028343389 hasAuthorship W2028343389A5080732397 @default.
• W2028343389 hasBestOaLocation W20283433891 @default.
• W2028343389 hasConcept C121332964 @default.
• W2028343389 hasConcept C168568712 @default.
• W2028343389 hasConcept C178635117 @default.
• W2028343389 hasConcept C185592680 @default.
• W2028343389 hasConcept C2777339483 @default.
• W2028343389 hasConcept C38652104 @default.
• W2028343389 hasConcept C41008148 @default.
• W2028343389 hasConcept C41999313 @default.
• W2028343389 hasConcept C44000306 @default.
• W2028343389 hasConcept C46141821 @default.
• W2028343389 hasConcept C521977710 @default.
• W2028343389 hasConcept C71240020 @default.
• W2028343389 hasConcept C74650414 @default.
• W2028343389 hasConcept C8010536 @default.
• W2028343389 hasConceptScore W2028343389C121332964 @default.
• W2028343389 hasConceptScore W2028343389C168568712 @default.
• W2028343389 hasConceptScore W2028343389C178635117 @default.
• W2028343389 hasConceptScore W2028343389C185592680 @default.
• W2028343389 hasConceptScore W2028343389C2777339483 @default.
• W2028343389 hasConceptScore W2028343389C38652104 @default.
• W2028343389 hasConceptScore W2028343389C41008148 @default.
• W2028343389 hasConceptScore W2028343389C41999313 @default.
• W2028343389 hasConceptScore W2028343389C44000306 @default.

• next