Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: The importance of binding site plasticity in protein–ligand interactions is ll-recognized, and so are the difficulties in predicting the nature and the degree of this plasticity by computational means. To assist in understanding the flexible protein–ligand interactions,  constructed the Pocketome, an encyclopedia of about one thousand experimentally solved conformational ensembles of druggable binding sites in proteins, grouped by location and consistent chain/cofactor composition. The multiplicity of pockets within the ensembles adds an extra, fourth dimension to the Pocketome entry data. Within each ensemble, the pockets re carefully classified by the degree of their pairwise similarity and compatibility with different ligands. The core of the Pocketome is derived regularly and automatically from the current releases of the Protein Data Bank and the Uniprot Knowledgebase; this core is complemented by entries built from manually provided seed ligand locations. The Pocketome bsite (www.pocketome.org) allows searching for the sites of interest, analysis of conformational clusters, important residues, binding compatibility matrices and interactive visualization of the ensembles using the ActiveICM b browser plugin. The Pocketome collection can be used to build multi-conformational docking and 3D activity models as ll as to design cross-docking and virtual ligand screening benchmarks.
['Irina Kufareva', 'Andrey V. Ilatovskiy', 'Ruben Abagyan']
I am writing a research paper on a idea Pocketome: an encyclopedia of small-molecule binding sites in 4D
[{"from": "human", "value": "I am writing a research paper on a idea Pocketome: an encyclopedia of small-molecule binding sites in 4D"}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: The importance of binding site plasticity in protein\u2013ligand interactions is ll-recognized, and so are the difficulties in predicting the nature and the degree of this plasticity by computational means. To assist in understanding the flexible protein\u2013ligand interactions,  constructed the Pocketome, an encyclopedia of about one thousand experimentally solved conformational ensembles of druggable binding sites in proteins, grouped by location and consistent chain/cofactor composition. The multiplicity of pockets within the ensembles adds an extra, fourth dimension to the Pocketome entry data. Within each ensemble, the pockets re carefully classified by the degree of their pairwise similarity and compatibility with different ligands. The core of the Pocketome is derived regularly and automatically from the current releases of the Protein Data Bank and the Uniprot Knowledgebase; this core is complemented by entries built from manually provided seed ligand locations. The Pocketome bsite (www.pocketome.org) allows searching for the sites of interest, analysis of conformational clusters, important residues, binding compatibility matrices and interactive visualization of the ensembles using the ActiveICM b browser plugin. The Pocketome collection can be used to build multi-conformational docking and 3D activity models as ll as to design cross-docking and virtual ligand screening benchmarks."}]