Accurate identification of structural features of ligand-protein binding is an essential step to characterizing the protein function and developing drugs with optimized sensitivity and specificity. BSP-SLIM is a blind molecular docking method on low-resolution protein structures. The method first identifies putative ligand binding sites by structurally matching the target to the template holo-structures. The ligand-protein docking conformation is then constructed by local shape and chemical feature complementarities between ligand and the negative image of binding pockets.
Click here to download example receptor and ligand structures.
- In this example, the receptor and ligand structures are an I-TASSER model of human deoxycytidine kinase and its ligand, gemcitabine, respectively.
- You can also see the BSP-SLIM output of the example structures here.
Hui Sun Lee and Yang Zhang.
BSP-SLIM: A blind low-resolution ligand-protein docking approach using theoretically predicted protein structures, Proteins, 2012, 80:93-110 (download the PDF file).