Molecular Modeling and Bioinformatics

LSHEBA (Local Structual Homology by Environment-Based Alignment)

Introduction

LSHEBA is a protein structure alignment procedure that finds and aligns regions of similar structures in two proteins. It searches and joins local strings of matched residues to obtain potential local alignments. Then it scores them with the score function considering sequence homology, similarity of secondary structure, and the accessibility of polar environment. LSHEBA can be used to find similar domains between proteins or defining domins themselves.