FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2103449051> ?p ?o ?g. }

• W2103449051 abstract "Calculations of electrostatic properties of protein-protein complexes are usually done within framework of a model with a certain set of parameters. In this paper we present a comprehensive statistical analysis of the sensitivity of the electrostatic component of binding free energy (DeltaDeltaGel) with respect with different force fields (Charmm, Amber, and OPLS), different values of the internal dielectric constant, and different presentations of molecular surface (different values of the probe radius). The study was done using the largest so far set of entries comprising 260 hetero and 2148 homo protein-protein complexes extracted from a previously developed database of protein complexes (ProtCom). To test the sensitivity of the energy calculations with respect to the structural details, all structures were energy minimized with corresponding force field, and the energies were recalculated. The results indicate that the absolute value of the electrostatic component of the binding free energy (DeltaDeltaGel) is very sensitive to the force field parameters, the minimization procedure, the values of the internal dielectric constant, and the probe radius. Nevertheless our results indicate that certain trends in DeltaDeltaGel behavior are much less sensitive to the calculation parameters. For instance, the fraction of the homo-complexes, for which the electrostatics was found to oppose binding, is 80% regardless of the force fields and parameters used. For the hetero-complexes, however, the percentage of the cases for which electrostatics opposed binding varied from 43% to 85%, depending on the protocol and parameters employed. A significant correlation was found between the effects caused by raising the internal dielectric constant and decreasing the probe radius. Correlations were also found among the results obtained with different force fields. However, despite of the correlations found, the absolute DeltaDeltaGel calculated with different force field parameters could differ more than tens of kcal/mol in some cases. Set of rules of obtaining confident predictions of absolute DeltaDeltaGel and DeltaDeltaGel sign are provided in the conclusion section.PACS codes: 87.15.A-, 87.15. km." @default.
• W2103449051 created "2016-06-24" @default.
• W2103449051 creator A5032623164 @default.
• W2103449051 creator A5050411996 @default.
• W2103449051 creator A5060030576 @default.
• W2103449051 creator A5075727451 @default.
• W2103449051 creator A5082048579 @default.
• W2103449051 date "2008-11-05" @default.
• W2103449051 modified "2023-10-08" @default.
• W2103449051 title "On the electrostatic component of protein-protein binding free energy" @default.
• W2103449051 cites W1534963014 @default.
• W2103449051 cites W1572013437 @default.
• W2103449051 cites W1625079248 @default.
• W2103449051 cites W1967712722 @default.
• W2103449051 cites W1977414257 @default.
• W2103449051 cites W1977496028 @default.
• W2103449051 cites W1977811526 @default.
• W2103449051 cites W1983853935 @default.
• W2103449051 cites W1987169321 @default.
• W2103449051 cites W1988152696 @default.
• W2103449051 cites W1989744452 @default.
• W2103449051 cites W1990287185 @default.
• W2103449051 cites W1990995713 @default.
• W2103449051 cites W1996451542 @default.
• W2103449051 cites W1998645872 @default.
• W2103449051 cites W2001939686 @default.
• W2103449051 cites W2003414919 @default.
• W2103449051 cites W2004145462 @default.
• W2103449051 cites W2010422957 @default.
• W2103449051 cites W2015649075 @default.
• W2103449051 cites W2019213007 @default.
• W2103449051 cites W2023504751 @default.
• W2103449051 cites W2027408247 @default.
• W2103449051 cites W2027626583 @default.
• W2103449051 cites W2031772330 @default.
• W2103449051 cites W2032590393 @default.
• W2103449051 cites W2035830350 @default.
• W2103449051 cites W2040816544 @default.
• W2103449051 cites W2041189078 @default.
• W2103449051 cites W2043062020 @default.
• W2103449051 cites W2043981631 @default.
• W2103449051 cites W2044170132 @default.
• W2103449051 cites W2047730466 @default.
• W2103449051 cites W2049704184 @default.
• W2103449051 cites W2051543023 @default.
• W2103449051 cites W2051628563 @default.
• W2103449051 cites W2053475844 @default.
• W2103449051 cites W2055607709 @default.
• W2103449051 cites W2057664120 @default.
• W2103449051 cites W2058527555 @default.
• W2103449051 cites W2063949927 @default.
• W2103449051 cites W2064924646 @default.
• W2103449051 cites W2067827057 @default.
• W2103449051 cites W2069079485 @default.
• W2103449051 cites W2071510805 @default.
• W2103449051 cites W2077503624 @default.
• W2103449051 cites W2078302553 @default.
• W2103449051 cites W2080727048 @default.
• W2103449051 cites W2084949662 @default.
• W2103449051 cites W2087574732 @default.
• W2103449051 cites W2090048857 @default.
• W2103449051 cites W2091916224 @default.
• W2103449051 cites W2093015919 @default.
• W2103449051 cites W2095841883 @default.
• W2103449051 cites W2096858057 @default.
• W2103449051 cites W2099505367 @default.
• W2103449051 cites W2101936319 @default.
• W2103449051 cites W2102640727 @default.
• W2103449051 cites W2104791350 @default.
• W2103449051 cites W2106320506 @default.
• W2103449051 cites W2108211735 @default.
• W2103449051 cites W2108975056 @default.
• W2103449051 cites W2110562802 @default.
• W2103449051 cites W2110928212 @default.
• W2103449051 cites W2114788392 @default.
• W2103449051 cites W2121166097 @default.
• W2103449051 cites W2125531202 @default.
• W2103449051 cites W2131713387 @default.
• W2103449051 cites W2139508887 @default.
• W2103449051 cites W2142843496 @default.
• W2103449051 cites W2144775933 @default.
• W2103449051 cites W2146686098 @default.
• W2103449051 cites W2147993766 @default.
• W2103449051 cites W2150123176 @default.
• W2103449051 cites W2153825083 @default.
• W2103449051 cites W2160341747 @default.
• W2103449051 cites W2161006313 @default.
• W2103449051 cites W2162166182 @default.
• W2103449051 cites W2170735624 @default.
• W2103449051 cites W2172082961 @default.
• W2103449051 cites W2177731497 @default.
• W2103449051 cites W2402268683 @default.
• W2103449051 doi "https://doi.org/10.1186/1757-5036-1-2" @default.
• W2103449051 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2666630" @default.
• W2103449051 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19351424" @default.
• W2103449051 hasPublicationYear "2008" @default.
• W2103449051 type Work @default.
• W2103449051 sameAs 2103449051 @default.
• W2103449051 citedByCount "45" @default.
• W2103449051 countsByYear W21034490512012 @default.

• next