GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

How Magnification of the Root-Mean-Square Deviation (RMSD) Value Affects the Convergence Speed of Hopfield Neural Network Classifier

The Root Mean Square-Deviation (RMSD) or Root Mean Square Error (RMSE) is the frequently used measure of the difference between values predicted by a model or an estimator and the values actually observed from that which is being modelled or estimated. In this paper, we show that the magnification of the RMSE, when used with the classifier Hopfield Neural Network (HNN), may help the network to ...

Accelerated protein structure comparison using TM-score-GPU

MOTIVATION Accurate comparisons of different protein structures play important roles in structural biology, structure prediction and functional annotation. The root-mean-square-deviation (RMSD) after optimal superposition is the predominant measure of similarity due to the ease and speed of computation. However, global RMSD is dependent on the length of the protein and can be dominated by diver...

On Weighted Pcm and Mean Square Deviation

Enhanced q-Least Mean Square

In this work, a new class of stochastic gradient algorithm is developed based on q-calculus. Unlike the existing q-LMS algorithm, the proposed approach fully utilizes the concept of q-calculus by incorporating time-varying q parameter. The proposed enhanced q-LMS (Eq-LMS) algorithm utilizes a novel, parameterless concept of error-correlation energy and normalization of signal to ensure high con...

Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA

The comparison and detection of the commonalities and differences in multiple structural ensembles is an important step in the use of molecular simulations to gain insight into the conformation and dynamics of complex biomacromolecules. While the average structure is often employed as the representative of an ensemble of structures in such comparisons, dynamic molecular systems with multiple co...