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QwikMD?-?Integrative Molecular Dynamics Toolkit for Novices and Experts.

ABSTRACT: The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.

SUBMITTER: Ribeiro JV

PROVIDER: S-EPMC4877583 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.

Ribeiro João V JV Bernardi Rafael C RC Rudack Till T Stone John E JE Phillips James C JC Freddolino Peter L PL Schulten Klaus K

Scientific reports 20160524

The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically r ...[more]

PMID: 27216779

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Project description:BackgroundPrincipal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized software to facilitate workflows and analysis of molecular dynamics simulation data to fully harness the power of PCA is lacking. The Java Essential Dynamics inspector (JEDi) software is a major upgrade from the previous JED software.ResultsEmploying multi-threading, JEDi features a user-friendly interface to control rapid workflows for interrogating conformational motions of biopolymers at various spatial resolutions and within subregions, including multiple chain proteins. JEDi has options for Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) to construct covariance (Q), correlation (R), and partial correlation (P) matrices. Shrinkage and outlier thresholding are implemented for the accurate estimation of covariance. The effect of rare events is quantified using outlier and inlier filters. Applying sparsity thresholds in statistical models identifies latent correlated motions. Within a hierarchical approach, small-scale atomic motion is first calculated with a separate local cPCA calculation per residue to obtain eigenresidues. Then PCA on the eigenresidues yields rapid and accurate description of large-scale motions. Local cPCA on all residue pairs creates a map of all residue-residue dynamical couplings. Additionally, kernel PCA is implemented. JEDi output gives high quality PNG images by default, with options for text files that include aligned coordinates, several metrics that quantify mobility, PCA modes with their eigenvalues, and displacement vector projections onto the top principal modes. JEDi provides PyMol scripts together with PDB files to visualize individual cPCA modes and the essential dynamics occurring within user-selected time scales. Subspace comparisons performed on the most relevant eigenvectors using several statistical metrics quantify similarity/overlap of high dimensional vector spaces. Free energy landscapes are available for both cPCA and dpPCA.ConclusionJEDi is a convenient toolkit that applies best practices in multivariate statistics for comparative studies on the essential dynamics of similar biopolymers. JEDi helps identify functional mechanisms through many integrated tools and visual aids for inspecting and quantifying similarity/differences in mobility and dynamic correlations.

Project description:Background: Abacus experts could mentally calculate fast some mathematical operations using multi-digit numbers. The temporal dynamics of abacus mental calculation are still unknown although some behavioral and neuroimaging studies have suggested a visuospatial and visuomotor neural process during abacus mental calculation. Therefore, this contribution aims to clarify the significant similarities and the differences between experts and novices by investigating calculation-induced neuromagnetic responses based on cerebral oscillatory changes. Methods: Twelve to 13 healthy abacus experts and 17 non-experts participated in two experimental paradigms using non-invasive neuromagnetic measurements. In experiments 1 and 2, the spatial distribution of oscillatory changes presented mental calculations and temporal frequency profiles during addition while examining multiplication tasks. The MEG data were analyzed using synthetic aperture magnetometry (SAM) with an adaptive beamformer to calculate the group average of the spatial distribution of oscillatory changes and their temporal frequency profiles in source-level analyses. Results: Using a group average of the spatial distribution of oscillatory changes, we observed some common brain activities in both right-handed abacus experts and non-experts. In non-experts, we detected the right dorsolateral prefrontal cortex (DLPFC) and bilateral Intraparietal sulcus (IPS); whereas in experts, detected the bilateral parieto-occipital sulcus (POS), right inferior frontal gyrus (IFG), and left sensorimotor areas mainly. Based on the findings generated, we could propose calculation processing models for both abacus experts and non- experts conveniently. Conclusion: The proposed model of calculation processing in abacus experts and novices revealed that the novices could calculate logically depending on numerical processing in the left IPS. In contrast, abacus experts are utilizing spatial processing using a memorized imaginary abacus, which distributed over the bilateral hemispheres in the IFG and sensorimotor areas.

Dataset Information

QwikMD?-?Integrative Molecular Dynamics Toolkit for Novices and Experts.

Publications

QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.

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