DALIX: Optimal DALI Protein Structure Alignment

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...

Dali: an algorithm for optimal structure alignment using distance matrices

Protein Structure Alignment Protein Structure Alignment

If we know the structures of the proteins A and B, and the function of protein A, then if we can detect structural similarity between A and B by producing an alignment between them, it can help us infer functionality of B. The problem of protein structure alignment is essentially similar to the sequence alignment; the fact that we have to do structural alignment in 3-d adds to the complexity of...

Discovering 3-d Protein Structures for Optimal Structure Alignment

Analyzing three dimensional protein structures is a very important task in molecular biology. Nowadays, the solution for protein structures often stems from the use of the state-of-the-art technologies such as nuclear magnetic resonance (NMR) spectroscopy techniques or X-Ray crystallography etc. as seen in the increasing number of PDB [34] entries. Protein Data Bank is a database of 3D structur...

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 ...