Abstract
Loop regions in proteins often play key roles in protein function because they participate in forming ligand or cofactor binding sites and enzyme active sites. In addition, the proportion of loops to a-helices/b-strands at active sites is known to be high. Therefore, to know where are functional site loops of a protein is a good start to understand the function of the protein.Due to these essential characteristics of loop, many studies have been carried out to understand the structure and function of various types of loops, and some methods for predicting the structure of loops were also developed. However, no specific method can be found to predict loops that are involved in the active site or the ligand/cofactor binding sites right now. Hence we tried to develop a method that can fulfill this need, and finally produced one, named FLOOP, which can select the active site loops or the ligand/cofactor binding sites loops of a protein from its sequence.The FLOOP method has been tested to select active site loops or ligand/cofactor binding site loops of many proteins, and the success rate is about 2-3 fold higher than a random guess. Besides, it is not a time-consuming method, which can provide a result in only 4 -5 second for a protein with ~1,200 amino acids. Furthermore, it also shows its potential to be used as a neutralizing antibody (Nab)-binding site prediction method, which makes this method more useful since there is also no specific method that is designed to predict Nab-binding sites of a protein.