FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W111431569> ?p ?o ?g. }

• W111431569 abstract "The prediction of important residues for binding/recognition sites in protein 3D structures is still a matter of challenge. Indeed, binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for the interaction with a specific ligand. In our group, we designed an innovative bioinformatics method called SuMo in order to detect similar 3-dimensional (3D) sites in proteins (Jambon et al. Protein-Struct Funct Genet 52:137–145, 2003). This approach allowed the comparison of protein structures or substructures, and detected local spatial similarities: the main advantage of the method is its independence for both amino acid sequences and backbone structures. In contrast to already existing tools, the basis for this method is a representation of the protein structure by a set of stereo chemical groups that are defined independently from the notion of amino acid. An efficient heuristics for finding similarities has been developed which uses graphs of triangles of chemical groups to represent the protein structures. The SuMo (Surfing the Molecules) program allows the dynamic definition of chemical groups, the selection of sites in the proteins, and the management and screening of databases. The basic principle of SuMo has been used in several recent studies (Sperandio et al. J Cheml Inf Model 47:1097–1110, 2007) (Doppelt-Azeroual et al. Protein Sci 19:847–867, 2010). In order to give access to the SuMo tool, we proposed a web server (Jambon et al. Bioinformatics 21:3929–3930, 2005) reachable at http://sumo-pbil.ibcp.fr. This chapter will describe the main rationale we initially took for designing the first release of SuMo. In addition, we propose a completely new set of parameters best suitable for proteins and finally, we illustrate its power with several biological examples. Two of them dealing with serine proteases and lectins are given for a comparison purpose. The first two examples illustrate the capability of SuMo to deal with completely opposite modes of evolution i.e. convergence and divergence. A new biological application dealing with betalactame binding protein PBB molecules is also presented." @default.
• W111431569 created "2016-06-24" @default.
• W111431569 creator A5003447220 @default.
• W111431569 creator A5009109452 @default.
• W111431569 creator A5028692767 @default.
• W111431569 creator A5070670765 @default.
• W111431569 creator A5071669171 @default.
• W111431569 creator A5078253318 @default.
• W111431569 date "2012-09-26" @default.
• W111431569 modified "2023-09-27" @default.
• W111431569 title "SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons" @default.
• W111431569 cites W1585234850 @default.
• W111431569 cites W1963513281 @default.
• W111431569 cites W1965533615 @default.
• W111431569 cites W1967293793 @default.
• W111431569 cites W1969001875 @default.
• W111431569 cites W1983742247 @default.
• W111431569 cites W1989713570 @default.
• W111431569 cites W2007978853 @default.
• W111431569 cites W2020202085 @default.
• W111431569 cites W2048089273 @default.
• W111431569 cites W2057350662 @default.
• W111431569 cites W2066880292 @default.
• W111431569 cites W2084681627 @default.
• W111431569 cites W2085833518 @default.
• W111431569 cites W2088979306 @default.
• W111431569 cites W2089499735 @default.
• W111431569 cites W2096039340 @default.
• W111431569 cites W2099013368 @default.
• W111431569 cites W2099182237 @default.
• W111431569 cites W2101909870 @default.
• W111431569 cites W2102535700 @default.
• W111431569 cites W2108302275 @default.
• W111431569 cites W2108617847 @default.
• W111431569 cites W2113149602 @default.
• W111431569 cites W2117164735 @default.
• W111431569 cites W2118517681 @default.
• W111431569 cites W2132395520 @default.
• W111431569 cites W2134306243 @default.
• W111431569 cites W2137167381 @default.
• W111431569 cites W2137345862 @default.
• W111431569 cites W2147437745 @default.
• W111431569 cites W2148068982 @default.
• W111431569 cites W2153251136 @default.
• W111431569 cites W2154033195 @default.
• W111431569 cites W2155744824 @default.
• W111431569 cites W2158714788 @default.
• W111431569 cites W2209906241 @default.
• W111431569 doi "https://doi.org/10.1007/978-94-007-5285-6_1" @default.
• W111431569 hasPublicationYear "2012" @default.
• W111431569 type Work @default.
• W111431569 sameAs 111431569 @default.
• W111431569 citedByCount "0" @default.
• W111431569 crossrefType "book-chapter" @default.
• W111431569 hasAuthorship W111431569A5003447220 @default.
• W111431569 hasAuthorship W111431569A5009109452 @default.
• W111431569 hasAuthorship W111431569A5028692767 @default.
• W111431569 hasAuthorship W111431569A5070670765 @default.
• W111431569 hasAuthorship W111431569A5071669171 @default.
• W111431569 hasAuthorship W111431569A5078253318 @default.
• W111431569 hasConcept C109095088 @default.
• W111431569 hasConcept C111919701 @default.
• W111431569 hasConcept C127705205 @default.
• W111431569 hasConcept C14036430 @default.
• W111431569 hasConcept C154945302 @default.
• W111431569 hasConcept C177264268 @default.
• W111431569 hasConcept C17744445 @default.
• W111431569 hasConcept C185592680 @default.
• W111431569 hasConcept C199360897 @default.
• W111431569 hasConcept C199539241 @default.
• W111431569 hasConcept C2776359362 @default.
• W111431569 hasConcept C41008148 @default.
• W111431569 hasConcept C47701112 @default.
• W111431569 hasConcept C54355233 @default.
• W111431569 hasConcept C55493867 @default.
• W111431569 hasConcept C70721500 @default.
• W111431569 hasConcept C86803240 @default.
• W111431569 hasConcept C94625758 @default.
• W111431569 hasConceptScore W111431569C109095088 @default.
• W111431569 hasConceptScore W111431569C111919701 @default.
• W111431569 hasConceptScore W111431569C127705205 @default.
• W111431569 hasConceptScore W111431569C14036430 @default.
• W111431569 hasConceptScore W111431569C154945302 @default.
• W111431569 hasConceptScore W111431569C177264268 @default.
• W111431569 hasConceptScore W111431569C17744445 @default.
• W111431569 hasConceptScore W111431569C185592680 @default.
• W111431569 hasConceptScore W111431569C199360897 @default.
• W111431569 hasConceptScore W111431569C199539241 @default.
• W111431569 hasConceptScore W111431569C2776359362 @default.
• W111431569 hasConceptScore W111431569C41008148 @default.
• W111431569 hasConceptScore W111431569C47701112 @default.
• W111431569 hasConceptScore W111431569C54355233 @default.
• W111431569 hasConceptScore W111431569C55493867 @default.
• W111431569 hasConceptScore W111431569C70721500 @default.
• W111431569 hasConceptScore W111431569C86803240 @default.
• W111431569 hasConceptScore W111431569C94625758 @default.
• W111431569 hasLocation W1114315691 @default.
• W111431569 hasOpenAccess W111431569 @default.
• W111431569 hasPrimaryLocation W1114315691 @default.
• W111431569 hasRelatedWork W2002263364 @default.

• next