Protein structure alignment beyond spatial proximity

Protein structure alignment beyond spatial proximity

Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologi...

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...

Bayesian Protein Structure Alignment.

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understandin...

Protein Structure Alphabetic Alignment

Fast Protein Structure Alignment

We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem’s intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worstcase analysis of the algorithm shows that the solution ...