Homology based structure extractor for protein structure prediction

The problem of protein structure prediction is one of the most complex problems in structural biology. The three groups of methods that attempt protein structure prediction are Homology modeling, Threading and Ab initio modeling. To predict the structure of a protein, homology modeling methods use structure details of proteins that are homologous to the query protein sequence. Two proteins are said to be homologous, if they are derived from the same ancestor and hence in most cases share similar structure and functions. In this paper we present a HOMology based structure EXtraction tool (HOMEX) that provides for a query sequence, the three-dimensional structure details of its homologous matches. The results provided by this tool can be used in homology based protein structure prediction methods to assign structure values of amino acids of the query sequence and can also be used in designing automated homologous modeling methods. HOMEX uses FASTA to search for homologous protein sequences and uses a specially designed dihedral angle database to extract structure details. To demonstrate the use of HOMEX in homology based protein structure prediction, we compared the results of HOMEX with the results of querying two different structure databases.