This paper proposes new algorithms for protein structure alignment. Protein structure alignment is, given two three-dimensional protein structures, to nd spatially equivalent residue pairs. Each algorithm consists of the following two steps: rst an initial superposition is computed; then a structure alignment is computed and re ned using bipartite graph matching. The proposed algorithms are sho...

Protein structure analysis is a very important research topic in the molecular biology of the post-genomic era. The root mean square deviation (RMSD) is the most frequently used measure for comparing two protein three-dimensional (3-D) structures. In this paper, we deal with two fundamental problems related to the RMSD. We first deal with a problem called the "range RMSD query" problem. Given a...

Root-mean-square-deviation (RMSD) is an indicator in protein-structure-prediction-algorithms (PSPAs). Goal of PSP algorithms is to obtain 0 Å RMSD from native protein structures. Protein structure and RMSD prediction is very essential. In 2013, the estimated RMSD proteins based on nine features were obtained best results using D2N (Distance to the native). We presented in This paper proposed ap...

This paper proposes new algorithms for protein structure alignment. Protein structure alignment is, given two three-dimensional protein structures, to nd spatially equivalent residue pairs. Each algorithm consists of the following two steps: rst an initial superposition is computed; then a structure alignment is computed and re ned using bipartite graph matching. The proposed algorithms are sho...

Root mean square deviation (RMSD) is often used to measure the difference between structures. We show mathematically that, for multiple structure alignment, the minimum RMSD (weighted at aligned positions or unweighted) for all pairs is the same as the RMSD to the average of the structures. Thus, using RMSD implies that the average is a consensus structure. We use this property to validate and ...

Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of "lagged RMSD-analysis" as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δ...

Motivation The root mean square deviation (RMSD) is one of the most used similarity criteria in structural biology and bioinformatics. Standard computation of the RMSD has a linear complexity with respect to the number of atoms in a molecule, making RMSD calculations time-consuming for the large-scale modeling applications, such as assessment of molecular docking predictions or clustering of sp...