Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach.

ABSTRACT: In order to identify the locations of metal ions in the binding sites of proteins, we have developed a method named the MADE (MAcromolecular DEnsity and Structure Analysis) approach. The MADE approach represents an evolution of our previous toolset, the ProBiS H₂O (MD) methodology, for the identification of conserved water molecules. Our method uses experimental structures of proteins homologous to a query, which are subsequently superimposed upon it. Areas with a particular species present in a similar location among many homologous protein structures are identified using a clustering algorithm. Dense clusters likely represent positions containing species important to the query protein structure or function. We analyze well-characterized apo protein structures and show t

SUBMITTER: Ravnik V 

PROVIDER: S-EPMC10466382 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature