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Center For Cancer Research National Cancer Institute
Molecular Modeling and Bioinformatics

RSE (Refinement with Seed Extension)

Introduction

RSE is a program that refines a given sequence alignment between 2 proteins whose structures are known. It does so by repeating a 2-step cycle. In step 1, the given sequence alignment is used to obtain optimal structural superposition using the mathematical procedure proposed by Kabsch in 1976 and 1978. In step 2, the SE algorithm is used to obtain optimal sequence alignment from the superposed structures.

RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional iterative refinement procedures based on residue-level dynamic programming algorithm in many structure alignment programs. A fuller report of the procedure is in BMC Bioinformatics 2009 10:210.