Identifying Active Site Cavities of Brain Derived Neurotrophic Factor Involved in Type II Diabetes

Active site prediction of BDNF is done to identify the locations of ligand binding sites and to predict functional similarities between cavities to estimate the locations of bound ligands. BDNF is a member of the neurotrophin family of growth factors, which are related to the canonical "Nerve Growth Factor", NGF. BDNF is a small dimeric protein which is abundantly and widely expressed in the adult mammalian brain. Various studies have shown possible links between BDNF and conditions, such as Diabetes, depression, schizophrenia, obsessive-compulsive disorder, Alzheimer's disease, Huntington's disease, Rett syndrome, and dementia, as well as anorexia nervosa and bulimia nervosa. Active site of BDNF is obtained by using active site prediction server. The cavity1 is identified as the cavity highest volume with the following amino acid sequence as the active site RTCEDFAIVKYSQGWLN the cavity points are 5.312Ao, 26.603Ao, 20.190Ao and the cavity volume is 1498 A3.