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Full-Text Articles in Bioinformatics
Automated Identification Of Binding Sites Forphosphorylated Ligands In Protein Structures, Dario Ghersi, Roberto Sanchez
Automated Identification Of Binding Sites Forphosphorylated Ligands In Protein Structures, Dario Ghersi, Roberto Sanchez
Interdisciplinary Informatics Faculty Publications
Phosphorylation is a crucial step in many cellular processes, ranging from metabolic reactions involved in energy transformation to signaling cascades. In many instances, protein domains specifically recognize the phosphogroup. Knowledge of the binding site provides insights into the interaction, and it can also be exploited for therapeutic purposes. Previous studies have shown that proteins interacting with phosphogroups are highly heterogeneous, and no single property can be used to reliably identify the binding site. Here we present an energy-based computational procedure that exploits the protein three-dimensional structure to identify binding sites involved in the recognition of phosphogroups. The procedure is validated …
Beyond Structural Genomics: Computational Approaches For The Identification Of Ligand Binding Sites In Protein Structures, Dario Ghersi, Roberto Sanchez
Beyond Structural Genomics: Computational Approaches For The Identification Of Ligand Binding Sites In Protein Structures, Dario Ghersi, Roberto Sanchez
Interdisciplinary Informatics Faculty Publications
t Structural genomics projects have revealed structures for a large number of proteins of unknown function. Understanding the interactions between these proteins and their ligands would provide an initial step in their functional characterization. Binding site identification methods are a fast and cost-effective way to facilitate the characterization of functionally important protein regions. In this review we describe our recently developed methods for binding site identification in the context of existing methods. The advantage of energy-based approaches is emphasized, since they provide flexibility in the identifi- cation and characterization of different types of binding sites