FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3209920439> ?p ?o ?g. }

• W3209920439 endingPage "731" @default.
• W3209920439 startingPage "720" @default.
• W3209920439 abstract "Predicting the quaternary structure of protein complex is an important problem. Inter-chain residue-residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter-chain contacts. Here, we develop the first method based on gradient descent optimization (GD) to build quaternary structures of protein dimers utilizing inter-chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true/predicted contacts and monomer structures as input. GD consistently performs better than both simulated annealing and Markov Chain Monte Carlo simulation. Starting from an arbitrarily quaternary structure randomly initialized from the tertiary structures of protein chains and using true inter-chain contacts as input, GD can reconstruct high-quality structural models for homodimers and heterodimers with average TM-score ranging from 0.92 to 0.99 and average interface root mean square distance from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter-chain contacts as restraints, the average TM-score of the structural models built by GD is 0.76. For 46% of the homodimers, high-quality structural models with TM-score ≥ 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. Only a moderate precision or recall of inter-chain contact prediction is needed to build good structural models for most homodimers. Moreover, GD improves the quality of quaternary structures predicted by AlphaFold2 on a Critical Assessment of Techniques for Protein Structure Prediction-Critical Assessments of Predictions of Interactions dataset." @default.
• W3209920439 created "2021-11-08" @default.
• W3209920439 creator A5000371339 @default.
• W3209920439 creator A5039246588 @default.
• W3209920439 creator A5044354277 @default.
• W3209920439 creator A5078026787 @default.
• W3209920439 creator A5090421599 @default.
• W3209920439 date "2021-11-02" @default.
• W3209920439 modified "2023-10-17" @default.
• W3209920439 title "Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts" @default.
• W3209920439 cites W1565809263 @default.
• W3209920439 cites W1965410913 @default.
• W3209920439 cites W1969679124 @default.
• W3209920439 cites W1970008650 @default.
• W3209920439 cites W1979762151 @default.
• W3209920439 cites W1981264193 @default.
• W3209920439 cites W1993951624 @default.
• W3209920439 cites W1995017064 @default.
• W3209920439 cites W2017421343 @default.
• W3209920439 cites W2019691413 @default.
• W3209920439 cites W2021343666 @default.
• W3209920439 cites W2045501270 @default.
• W3209920439 cites W2051434435 @default.
• W3209920439 cites W2055905702 @default.
• W3209920439 cites W2073911195 @default.
• W3209920439 cites W2083898222 @default.
• W3209920439 cites W2097698280 @default.
• W3209920439 cites W2102245393 @default.
• W3209920439 cites W2107867854 @default.
• W3209920439 cites W2110720709 @default.
• W3209920439 cites W2111387452 @default.
• W3209920439 cites W2112743424 @default.
• W3209920439 cites W2120836664 @default.
• W3209920439 cites W2128674962 @default.
• W3209920439 cites W2129454543 @default.
• W3209920439 cites W2133712572 @default.
• W3209920439 cites W2139373949 @default.
• W3209920439 cites W2140615634 @default.
• W3209920439 cites W2148219066 @default.
• W3209920439 cites W2149525061 @default.
• W3209920439 cites W2153255725 @default.
• W3209920439 cites W2153731681 @default.
• W3209920439 cites W2153954618 @default.
• W3209920439 cites W2153983456 @default.
• W3209920439 cites W2158945625 @default.
• W3209920439 cites W2160223331 @default.
• W3209920439 cites W2163614321 @default.
• W3209920439 cites W2343238565 @default.
• W3209920439 cites W2508425869 @default.
• W3209920439 cites W2514282803 @default.
• W3209920439 cites W2804651207 @default.
• W3209920439 cites W2915344963 @default.
• W3209920439 cites W2951639995 @default.
• W3209920439 cites W2967606876 @default.
• W3209920439 cites W2971733377 @default.
• W3209920439 cites W2995531725 @default.
• W3209920439 cites W2997234557 @default.
• W3209920439 cites W2999044305 @default.
• W3209920439 cites W3072197457 @default.
• W3209920439 cites W3106340289 @default.
• W3209920439 cites W3124030253 @default.
• W3209920439 cites W3133540795 @default.
• W3209920439 cites W3177828909 @default.
• W3209920439 cites W3186340132 @default.
• W3209920439 cites W3193795503 @default.
• W3209920439 cites W3201523886 @default.
• W3209920439 cites W3209920439 @default.
• W3209920439 cites W4210646117 @default.
• W3209920439 doi "https://doi.org/10.1002/prot.26269" @default.
• W3209920439 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34716620" @default.
• W3209920439 hasPublicationYear "2021" @default.
• W3209920439 type Work @default.
• W3209920439 sameAs 3209920439 @default.
• W3209920439 citedByCount "5" @default.
• W3209920439 countsByYear W32099204392021 @default.
• W3209920439 countsByYear W32099204392022 @default.
• W3209920439 countsByYear W32099204392023 @default.
• W3209920439 crossrefType "journal-article" @default.
• W3209920439 hasAuthorship W3209920439A5000371339 @default.
• W3209920439 hasAuthorship W3209920439A5039246588 @default.
• W3209920439 hasAuthorship W3209920439A5044354277 @default.
• W3209920439 hasAuthorship W3209920439A5078026787 @default.
• W3209920439 hasAuthorship W3209920439A5090421599 @default.
• W3209920439 hasBestOaLocation W32099204395 @default.
• W3209920439 hasConcept C104292427 @default.
• W3209920439 hasConcept C104317684 @default.
• W3209920439 hasConcept C11413529 @default.
• W3209920439 hasConcept C115051666 @default.
• W3209920439 hasConcept C119857082 @default.
• W3209920439 hasConcept C121332964 @default.
• W3209920439 hasConcept C126980161 @default.
• W3209920439 hasConcept C1276947 @default.
• W3209920439 hasConcept C147597530 @default.
• W3209920439 hasConcept C151730666 @default.
• W3209920439 hasConcept C160464908 @default.
• W3209920439 hasConcept C18051474 @default.
• W3209920439 hasConcept C185592680 @default.
• W3209920439 hasConcept C186060115 @default.

• next