Matches in SemOpenAlex for { <https://semopenalex.org/work/W2521118018> ?p ?o ?g. }
Showing items 1 to 81 of
81
with 100 items per page.
- W2521118018 abstract "Author(s): Spitzer, Russell Alexander | Advisor(s): Jain, Ajay N | Abstract: Protein similarity has been used for the annotation and classification of proteins when the structure of the protein is available. Protein similarity comparisons may be made on a local or global basis and may consider sequence information and differing levels of structural information. This dissertation details the method Surflex PSIM, a local 3D method that compares the surfaces of protein binding sites. PSIM is a local 3D method that compares protein binding site surfaces in full atomic detail. The approach is based on the morphological similarity method (Surflex-Sim) which has been widely applied for global comparison of small molecules. This methodology has the ability to determine the differences between very similar proteins with different ligand binding specificity and the ability to correctly align extremely divergent proteins with only a small region of similarity. PSIM performed well on known standards for binding site comparisons. In a docking benchmark study, PSIM was used to assist in multi-structure docking protocols. In these protocols, proper selection of target structures can reduce time required for screening and increase accuracy. Selection of a minimal representative set of docking target conformations was performed automatically using PSIM. Several docking targets, for which unsatisfactory results had been obtained used a single-structure protocol, yielded substantial improvements using the PSIM-aided multi-structure docking protocol. Further development of an automated binding-site detection algorithm allowed for PSIM to be used as screening tool for annotating proteins with unknown function. A dataset was created of proteins whose function was determined after their crystallization. PSIM was able to automatically detect binding sites on a majority of these proteins and successfully match them to proteins that were present in the PDB at the time of crystallization that have the same function. PSIM was further used to explore possible functions for several proteins whose function is still unknown. The main contribution of this dissertation is a fast and accurate method for the comparison of protein binding sites agnostic of sequence information. This methodology has applications in the analysis of ligand specificity analysis and the annotation of proteins with unknown function." @default.
- W2521118018 created "2016-09-30" @default.
- W2521118018 creator A5062055990 @default.
- W2521118018 date "2013-01-01" @default.
- W2521118018 modified "2023-09-27" @default.
- W2521118018 title "Applications of a Surface-Based Protein Binding Site Comparison Methodology" @default.
- W2521118018 hasPublicationYear "2013" @default.
- W2521118018 type Work @default.
- W2521118018 sameAs 2521118018 @default.
- W2521118018 citedByCount "0" @default.
- W2521118018 crossrefType "journal-article" @default.
- W2521118018 hasAuthorship W2521118018A5062055990 @default.
- W2521118018 hasConcept C103278499 @default.
- W2521118018 hasConcept C103697762 @default.
- W2521118018 hasConcept C107824862 @default.
- W2521118018 hasConcept C115961682 @default.
- W2521118018 hasConcept C13280743 @default.
- W2521118018 hasConcept C139489369 @default.
- W2521118018 hasConcept C147597530 @default.
- W2521118018 hasConcept C154945302 @default.
- W2521118018 hasConcept C159110408 @default.
- W2521118018 hasConcept C185592680 @default.
- W2521118018 hasConcept C185798385 @default.
- W2521118018 hasConcept C186060115 @default.
- W2521118018 hasConcept C205649164 @default.
- W2521118018 hasConcept C41008148 @default.
- W2521118018 hasConcept C41685203 @default.
- W2521118018 hasConcept C55493867 @default.
- W2521118018 hasConcept C59593255 @default.
- W2521118018 hasConcept C70721500 @default.
- W2521118018 hasConcept C71924100 @default.
- W2521118018 hasConcept C77319485 @default.
- W2521118018 hasConcept C86803240 @default.
- W2521118018 hasConceptScore W2521118018C103278499 @default.
- W2521118018 hasConceptScore W2521118018C103697762 @default.
- W2521118018 hasConceptScore W2521118018C107824862 @default.
- W2521118018 hasConceptScore W2521118018C115961682 @default.
- W2521118018 hasConceptScore W2521118018C13280743 @default.
- W2521118018 hasConceptScore W2521118018C139489369 @default.
- W2521118018 hasConceptScore W2521118018C147597530 @default.
- W2521118018 hasConceptScore W2521118018C154945302 @default.
- W2521118018 hasConceptScore W2521118018C159110408 @default.
- W2521118018 hasConceptScore W2521118018C185592680 @default.
- W2521118018 hasConceptScore W2521118018C185798385 @default.
- W2521118018 hasConceptScore W2521118018C186060115 @default.
- W2521118018 hasConceptScore W2521118018C205649164 @default.
- W2521118018 hasConceptScore W2521118018C41008148 @default.
- W2521118018 hasConceptScore W2521118018C41685203 @default.
- W2521118018 hasConceptScore W2521118018C55493867 @default.
- W2521118018 hasConceptScore W2521118018C59593255 @default.
- W2521118018 hasConceptScore W2521118018C70721500 @default.
- W2521118018 hasConceptScore W2521118018C71924100 @default.
- W2521118018 hasConceptScore W2521118018C77319485 @default.
- W2521118018 hasConceptScore W2521118018C86803240 @default.
- W2521118018 hasLocation W25211180181 @default.
- W2521118018 hasOpenAccess W2521118018 @default.
- W2521118018 hasPrimaryLocation W25211180181 @default.
- W2521118018 hasRelatedWork W121225143 @default.
- W2521118018 hasRelatedWork W1758070551 @default.
- W2521118018 hasRelatedWork W1988575626 @default.
- W2521118018 hasRelatedWork W1990403339 @default.
- W2521118018 hasRelatedWork W2040595595 @default.
- W2521118018 hasRelatedWork W2059215264 @default.
- W2521118018 hasRelatedWork W2060387125 @default.
- W2521118018 hasRelatedWork W2101557653 @default.
- W2521118018 hasRelatedWork W2123007244 @default.
- W2521118018 hasRelatedWork W2123764626 @default.
- W2521118018 hasRelatedWork W2131989561 @default.
- W2521118018 hasRelatedWork W2140058398 @default.
- W2521118018 hasRelatedWork W2154813243 @default.
- W2521118018 hasRelatedWork W2162682281 @default.
- W2521118018 hasRelatedWork W2164059036 @default.
- W2521118018 hasRelatedWork W2171173309 @default.
- W2521118018 hasRelatedWork W2423377342 @default.
- W2521118018 hasRelatedWork W2750875483 @default.
- W2521118018 hasRelatedWork W2799682268 @default.
- W2521118018 hasRelatedWork W2937388783 @default.
- W2521118018 isParatext "false" @default.
- W2521118018 isRetracted "false" @default.
- W2521118018 magId "2521118018" @default.
- W2521118018 workType "article" @default.