FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2099045471> ?p ?o ?g. }

• W2099045471 abstract "Abstract Computational protein‐protein docking scans commonly produce correct and nearly correct interaction models, but sometimes these models are ranked low. We present here postscan processing procedures that dramatically enhance the distinction between nearly correct and false predictions. The procedures employ propensity descriptors calculated for the interface core, an interface‐core clusters count, solvation energy, and a geometric‐electrostatic‐hydrophobic complementarity score. The various descriptors rank high different selections of false models (shuffling effect), and therefore, are used as Boolean yes/no classifiers in “soft intersection” filters, which eliminate large proportions of false models. Furthermore, the standardized descriptors are used in new scoring functions that highlight nearly correct models (NCMs). All the tests are performed on unbound docking models produced with MolFit without use of external data. We find that the discrimination between nearly correct and false models by the various descriptors is class dependent; hence, our postscan processing is class specific. The filters reduce the number of putative models from 10,726, 12,517, and 11,054 to 758, 157, and 1218 for enzyme‐inhibitor, antibody‐antigen, and nonclassified systems. When combined with the new scoring functions, they improve the average rank of the highest ranking NCMs from 673 to 122. Application to 23 CAPRI targets demonstrates the effectiveness of the postscan procedures in cases where external information is used in the production of the putative models. Our new per‐molecule residue propensity descriptors show that interacting interfaces are enriched with high propensity residues except for antigenic sites, which resemble more the noninteracting regions of protein surfaces. Proteins 2009. © 2009 Wiley‐Liss, Inc." @default.
• W2099045471 created "2016-06-24" @default.
• W2099045471 creator A5028551465 @default.
• W2099045471 creator A5085947500 @default.
• W2099045471 date "2009-05-18" @default.
• W2099045471 modified "2023-09-30" @default.
• W2099045471 title "Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models" @default.
• W2099045471 cites W1526151739 @default.
• W2099045471 cites W1548566593 @default.
• W2099045471 cites W1550449038 @default.
• W2099045471 cites W1792865908 @default.
• W2099045471 cites W1926568554 @default.
• W2099045471 cites W1968922152 @default.
• W2099045471 cites W1970119605 @default.
• W2099045471 cites W1973581737 @default.
• W2099045471 cites W1983851480 @default.
• W2099045471 cites W1985153601 @default.
• W2099045471 cites W1987749411 @default.
• W2099045471 cites W1992176724 @default.
• W2099045471 cites W1992259266 @default.
• W2099045471 cites W1992657945 @default.
• W2099045471 cites W2000383223 @default.
• W2099045471 cites W2002112906 @default.
• W2099045471 cites W2005049999 @default.
• W2099045471 cites W2006398943 @default.
• W2099045471 cites W2006684024 @default.
• W2099045471 cites W2011851849 @default.
• W2099045471 cites W2012173264 @default.
• W2099045471 cites W2014744153 @default.
• W2099045471 cites W2018337406 @default.
• W2099045471 cites W2025120281 @default.
• W2099045471 cites W2026210802 @default.
• W2099045471 cites W2030154259 @default.
• W2099045471 cites W2031772330 @default.
• W2099045471 cites W2032059503 @default.
• W2099045471 cites W2032260773 @default.
• W2099045471 cites W2033362014 @default.
• W2099045471 cites W2035503835 @default.
• W2099045471 cites W2036841131 @default.
• W2099045471 cites W2046736165 @default.
• W2099045471 cites W2047994201 @default.
• W2099045471 cites W2048643046 @default.
• W2099045471 cites W2051710717 @default.
• W2099045471 cites W2053738633 @default.
• W2099045471 cites W2056034415 @default.
• W2099045471 cites W2058017150 @default.
• W2099045471 cites W2061661303 @default.
• W2099045471 cites W2065578811 @default.
• W2099045471 cites W2067598924 @default.
• W2099045471 cites W2068115563 @default.
• W2099045471 cites W2072162021 @default.
• W2099045471 cites W2074421004 @default.
• W2099045471 cites W2075770210 @default.
• W2099045471 cites W2078302553 @default.
• W2099045471 cites W2081290596 @default.
• W2099045471 cites W2083995470 @default.
• W2099045471 cites W2084949662 @default.
• W2099045471 cites W2088542339 @default.
• W2099045471 cites W2091565674 @default.
• W2099045471 cites W2091734240 @default.
• W2099045471 cites W2094148990 @default.
• W2099045471 cites W2095157453 @default.
• W2099045471 cites W2098110345 @default.
• W2099045471 cites W2103210604 @default.
• W2099045471 cites W2103644587 @default.
• W2099045471 cites W2104686275 @default.
• W2099045471 cites W2111387452 @default.
• W2099045471 cites W2116515668 @default.
• W2099045471 cites W2117584882 @default.
• W2099045471 cites W2120412820 @default.
• W2099045471 cites W2121166097 @default.
• W2099045471 cites W2124036707 @default.
• W2099045471 cites W2128039232 @default.
• W2099045471 cites W2129414710 @default.
• W2099045471 cites W2129454543 @default.
• W2099045471 cites W2133842820 @default.
• W2099045471 cites W2136206140 @default.
• W2099045471 cites W2136525667 @default.
• W2099045471 cites W2137167381 @default.
• W2099045471 cites W2137321308 @default.
• W2099045471 cites W2139074914 @default.
• W2099045471 cites W2139853103 @default.
• W2099045471 cites W2141438296 @default.
• W2099045471 cites W2142747988 @default.
• W2099045471 cites W2149984099 @default.
• W2099045471 cites W2151468502 @default.
• W2099045471 cites W2157892451 @default.
• W2099045471 cites W2158100564 @default.
• W2099045471 cites W2159192638 @default.
• W2099045471 cites W2160868144 @default.
• W2099045471 cites W2162502996 @default.
• W2099045471 cites W2170110204 @default.
• W2099045471 cites W2170872475 @default.
• W2099045471 cites W2171249995 @default.
• W2099045471 cites W2171516325 @default.
• W2099045471 cites W4253436731 @default.
• W2099045471 doi "https://doi.org/10.1002/prot.22436" @default.
• W2099045471 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19452551" @default.
• W2099045471 hasPublicationYear "2009" @default.
• W2099045471 type Work @default.

• next