FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2091796735> ?p ?o ?g. }

• W2091796735 endingPage "51" @default.
• W2091796735 startingPage "38" @default.
• W2091796735 abstract "Abstract Availability of energy functions which can discriminate native‐like from non‐native protein conformations is crucial for theoretical protein structure prediction and refinement of low‐resolution protein models. This article reports the results of benchmark tests for scoring functions based on two all‐atom ECEPP force fields, that is, ECEPP/3 and ECEPP05, and two implicit solvent models for a large set of protein decoys. The following three scoring functions are considered: (i) ECEPP05 plus a solvent‐accessible surface area model with the parameters optimized with a set of protein decoys (ECEPP05/SA); (ii) ECEPP/3 plus the solvent‐accessible surface area model of Ooi et al . (Proc Natl Acad Sci USA 1987;84:3086–3090) (ECEPP3/OONS); and (iii) ECEPP05 plus an implicit solvent model based on a solution of the Poisson equation with an optimized Fast Adaptive Multigrid Boundary Element (FAMBEpH) method (ECEPP05/FAMBEpH). Short Monte Carlo‐with‐Minimization (MCM) simulations, following local energy minimization, are used as a scoring method with ECEPP05/SA and ECEPP3/OONS potentials, whereas energy calculation is used with ECEPP05/FAMBEpH. The performance of each scoring function is evaluated by examining its ability to distinguish between native‐like and non‐native protein structures. The results of the tests show that the new ECEPP05/SA scoring function represents a significant improvement over the earlier ECEPP3/OONS version of the force field. Thus, it is able to rank native‐like structures with C α root‐mean‐square‐deviations below 3.5 Å as lowest‐energy conformations for 76% and within the top 10 for 87% of the proteins tested, compared with 69 and 80%, respectively, for ECEPP3/OONS. The use of the FAMBEpH solvation model, which provides a more accurate description of the protein‐solvent interactions, improves the discriminative ability of the scoring function to 89%. All failed tests in which the native‐like structures cannot be discriminated as those with low energy, are due to omission of protein–protein interactions. The results of this study represent a benchmark in force‐field development, and may be useful for evaluation of the performance of different force fields. Proteins 2009. © 2009 Wiley‐Liss, Inc." @default.
• W2091796735 created "2016-06-24" @default.
• W2091796735 creator A5004927601 @default.
• W2091796735 creator A5022665888 @default.
• W2091796735 creator A5051306238 @default.
• W2091796735 creator A5087430326 @default.
• W2091796735 date "2009-04-21" @default.
• W2091796735 modified "2023-10-17" @default.
• W2091796735 title "Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation" @default.
• W2091796735 cites W1965680834 @default.
• W2091796735 cites W1966029728 @default.
• W2091796735 cites W1968543088 @default.
• W2091796735 cites W1972772174 @default.
• W2091796735 cites W1980003947 @default.
• W2091796735 cites W1995204277 @default.
• W2091796735 cites W1995260626 @default.
• W2091796735 cites W1998618677 @default.
• W2091796735 cites W1999347494 @default.
• W2091796735 cites W2002963645 @default.
• W2091796735 cites W2004461664 @default.
• W2091796735 cites W2007135643 @default.
• W2091796735 cites W2007519896 @default.
• W2091796735 cites W2013785414 @default.
• W2091796735 cites W2023477917 @default.
• W2091796735 cites W2025300651 @default.
• W2091796735 cites W2027408247 @default.
• W2091796735 cites W2028227377 @default.
• W2091796735 cites W2029087609 @default.
• W2091796735 cites W2029699793 @default.
• W2091796735 cites W2035203406 @default.
• W2091796735 cites W2037603210 @default.
• W2091796735 cites W2040823078 @default.
• W2091796735 cites W2045777307 @default.
• W2091796735 cites W2052112948 @default.
• W2091796735 cites W2053028650 @default.
• W2091796735 cites W2054881399 @default.
• W2091796735 cites W2062081085 @default.
• W2091796735 cites W2069123478 @default.
• W2091796735 cites W2080396507 @default.
• W2091796735 cites W2094051420 @default.
• W2091796735 cites W2094087249 @default.
• W2091796735 cites W2097969975 @default.
• W2091796735 cites W2105706802 @default.
• W2091796735 cites W2111098051 @default.
• W2091796735 cites W2114722917 @default.
• W2091796735 cites W2122199548 @default.
• W2091796735 cites W2126084959 @default.
• W2091796735 cites W2129509556 @default.
• W2091796735 cites W2130479394 @default.
• W2091796735 cites W2131169717 @default.
• W2091796735 cites W2133230269 @default.
• W2091796735 cites W2139281871 @default.
• W2091796735 cites W2141920824 @default.
• W2091796735 cites W2144739764 @default.
• W2091796735 cites W2156393161 @default.
• W2091796735 cites W2168107543 @default.
• W2091796735 cites W2997715027 @default.
• W2091796735 cites W4235954223 @default.
• W2091796735 cites W4302592293 @default.
• W2091796735 doi "https://doi.org/10.1002/prot.22414" @default.
• W2091796735 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4502597" @default.
• W2091796735 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19384995" @default.
• W2091796735 hasPublicationYear "2009" @default.
• W2091796735 type Work @default.
• W2091796735 sameAs 2091796735 @default.
• W2091796735 citedByCount "22" @default.
• W2091796735 countsByYear W20917967352012 @default.
• W2091796735 countsByYear W20917967352014 @default.
• W2091796735 countsByYear W20917967352015 @default.
• W2091796735 countsByYear W20917967352016 @default.
• W2091796735 countsByYear W20917967352017 @default.
• W2091796735 countsByYear W20917967352018 @default.
• W2091796735 countsByYear W20917967352019 @default.
• W2091796735 countsByYear W20917967352022 @default.
• W2091796735 countsByYear W20917967352023 @default.
• W2091796735 crossrefType "journal-article" @default.
• W2091796735 hasAuthorship W2091796735A5004927601 @default.
• W2091796735 hasAuthorship W2091796735A5022665888 @default.
• W2091796735 hasAuthorship W2091796735A5051306238 @default.
• W2091796735 hasAuthorship W2091796735A5087430326 @default.
• W2091796735 hasBestOaLocation W20917967352 @default.
• W2091796735 hasConcept C10803110 @default.
• W2091796735 hasConcept C11413529 @default.
• W2091796735 hasConcept C121332964 @default.
• W2091796735 hasConcept C121864883 @default.
• W2091796735 hasConcept C147597530 @default.
• W2091796735 hasConcept C154945302 @default.
• W2091796735 hasConcept C15744967 @default.
• W2091796735 hasConcept C185592680 @default.
• W2091796735 hasConcept C2776029896 @default.
• W2091796735 hasConcept C28826006 @default.
• W2091796735 hasConcept C33923547 @default.
• W2091796735 hasConcept C41008148 @default.
• W2091796735 hasConcept C77805123 @default.
• W2091796735 hasConcept C97355855 @default.
• W2091796735 hasConceptScore W2091796735C10803110 @default.
• W2091796735 hasConceptScore W2091796735C11413529 @default.
• W2091796735 hasConceptScore W2091796735C121332964 @default.

• next