FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2019706247> ?p ?o ?g. }

• W2019706247 endingPage "1153" @default.
• W2019706247 startingPage "1143" @default.
• W2019706247 abstract "Abstract In this and the accompanying article, we report the development of new physics‐based side‐chain‐rotamer and virtual‐bond‐deformation potentials which now replace the respective statistical potentials used so far in our physics‐based united‐reside UNRES force field for large‐scale simulations of protein structure and dynamics. In this article, we describe the methodology for determining the corresponding potentials of mean force (PMF's) from the energy surfaces of terminally‐blocked amino‐acid residues calculated with the AM1 quantum‐mechanical semiempirical method. The approach is based on minimization of the AM1 energy for fixed values of the angles λ for rotation of the peptide groups about the C α ··· C α virtual bonds, and for fixed values of the side‐chain dihedral angles χ, which formed a multidimensional grid. A harmonic‐approximation approach was developed to extrapolate from the energy at a given grid point to other points of the conformational space to compute the respective contributions to the PMF. To test the applicability of the harmonic approximation, the rotamer PMF's of alanine and valine obtained with this approach have been compared with those obtained by using a Metropolis Monte Carlo method. The PMF surfaces computed with the harmonic approximation are more rugged and have more pronounced minima than the MC‐calculated surfaces but the harmonic‐approximation‐and MC‐calculated PMF values are linearly correlated. The potentials derived with the harmonic approximation are, therefore, appropriate for UNRES for which the weights (scaling factors) of the energy terms are determined by force‐field optimization for foldability. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010" @default.
• W2019706247 created "2016-06-24" @default.
• W2019706247 creator A5022665888 @default.
• W2019706247 creator A5052827727 @default.
• W2019706247 creator A5091855436 @default.
• W2019706247 date "2010-01-13" @default.
• W2019706247 modified "2023-10-10" @default.
• W2019706247 title "Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method" @default.
• W2019706247 cites W102295232 @default.
• W2019706247 cites W1964066268 @default.
• W2019706247 cites W1966041739 @default.
• W2019706247 cites W1970984671 @default.
• W2019706247 cites W1972379241 @default.
• W2019706247 cites W1973858832 @default.
• W2019706247 cites W1975205107 @default.
• W2019706247 cites W1981532742 @default.
• W2019706247 cites W1981909452 @default.
• W2019706247 cites W1985402094 @default.
• W2019706247 cites W1990891161 @default.
• W2019706247 cites W1993985257 @default.
• W2019706247 cites W2001956250 @default.
• W2019706247 cites W2009133700 @default.
• W2019706247 cites W2010562586 @default.
• W2019706247 cites W2011734083 @default.
• W2019706247 cites W2011805684 @default.
• W2019706247 cites W2016832940 @default.
• W2019706247 cites W2017562024 @default.
• W2019706247 cites W2021438484 @default.
• W2019706247 cites W2023041802 @default.
• W2019706247 cites W2024759709 @default.
• W2019706247 cites W2028263411 @default.
• W2019706247 cites W2028276552 @default.
• W2019706247 cites W2031613369 @default.
• W2019706247 cites W2033570280 @default.
• W2019706247 cites W2033586482 @default.
• W2019706247 cites W2034101016 @default.
• W2019706247 cites W2034190349 @default.
• W2019706247 cites W2036239645 @default.
• W2019706247 cites W2048595293 @default.
• W2019706247 cites W2049650691 @default.
• W2019706247 cites W2055563809 @default.
• W2019706247 cites W2056760934 @default.
• W2019706247 cites W2060036077 @default.
• W2019706247 cites W2062105576 @default.
• W2019706247 cites W2074050984 @default.
• W2019706247 cites W2075403140 @default.
• W2019706247 cites W2075574523 @default.
• W2019706247 cites W2075771614 @default.
• W2019706247 cites W2076368603 @default.
• W2019706247 cites W2085764610 @default.
• W2019706247 cites W2087149342 @default.
• W2019706247 cites W2088488932 @default.
• W2019706247 cites W2090847673 @default.
• W2019706247 cites W2093894241 @default.
• W2019706247 cites W2095111795 @default.
• W2019706247 cites W2103230617 @default.
• W2019706247 cites W2106619251 @default.
• W2019706247 cites W2111481173 @default.
• W2019706247 cites W2118250094 @default.
• W2019706247 cites W2126157913 @default.
• W2019706247 cites W2134812230 @default.
• W2019706247 cites W2139236870 @default.
• W2019706247 cites W2142694980 @default.
• W2019706247 cites W2151414656 @default.
• W2019706247 cites W2151819067 @default.
• W2019706247 cites W230227022 @default.
• W2019706247 doi "https://doi.org/10.1002/jcc.21399" @default.
• W2019706247 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2841724" @default.
• W2019706247 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/20073062" @default.
• W2019706247 hasPublicationYear "2010" @default.
• W2019706247 type Work @default.
• W2019706247 sameAs 2019706247 @default.
• W2019706247 citedByCount "8" @default.
• W2019706247 countsByYear W20197062472014 @default.
• W2019706247 countsByYear W20197062472015 @default.
• W2019706247 countsByYear W20197062472021 @default.
• W2019706247 countsByYear W20197062472022 @default.
• W2019706247 crossrefType "journal-article" @default.
• W2019706247 hasAuthorship W2019706247A5022665888 @default.
• W2019706247 hasAuthorship W2019706247A5052827727 @default.
• W2019706247 hasAuthorship W2019706247A5091855436 @default.
• W2019706247 hasBestOaLocation W20197062472 @default.
• W2019706247 hasConcept C10803110 @default.
• W2019706247 hasConcept C112887158 @default.
• W2019706247 hasConcept C121332964 @default.
• W2019706247 hasConcept C121864883 @default.
• W2019706247 hasConcept C125277925 @default.
• W2019706247 hasConcept C127934551 @default.
• W2019706247 hasConcept C134306372 @default.
• W2019706247 hasConcept C147597530 @default.
• W2019706247 hasConcept C14961307 @default.
• W2019706247 hasConcept C185592680 @default.
• W2019706247 hasConcept C186633575 @default.
• W2019706247 hasConcept C18705241 @default.
• W2019706247 hasConcept C193547582 @default.
• W2019706247 hasConcept C2524010 @default.
• W2019706247 hasConcept C2781442258 @default.
• W2019706247 hasConcept C32909587 @default.

• next