Algorithm engineering for optimal alignment of protein structure distance matrices

Algorithm engineering for optimal alignment of protein structure distance matrices

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special case...

Dali: an algorithm for optimal structure alignment using distance matrices

Towards optimal alignment of protein structure distance matrices

MOTIVATION Structural alignments of proteins are important for identification of structural similarities, homology detection and functional annotation. The structural alignment problem is well studied and computationally difficult. Many different scoring schemes for structural similarity as well as many algorithms for finding high-scoring alignments have been proposed. Algorithms using contact ...

Optimal DALI protein structure alignment

We present a mathematical model and exact algorithm for protein structure alignment using dali scoring, which is an NP-hard problem. dali scoring is based on comparing the inter-residue distance matrices of proteins and is the scoring model of the widely used heuristic dali program. Our model and algorithm extend an integer linear programming approach previously used for the related contact map...

A Parameterized Algorithm for Protein Structure Alignment

This paper proposes a parameterized polynomial time approximation scheme (PTAS) for aligning two protein structures, in the case where one protein structure is represented by a contact map graph and the other by a contact map graph or a distance matrix. If the sequential order of alignment is not required, the time complexity is polynomial in the protein size and exponential with respect to two...