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3 results for “Normal Mode Analysis”
Supplementary data frames, AlphaFold models, Normal Mode Analysis (NMA) Data, and NMA of Corresponding NMR Ensembles in the S2RCI, MD, and S2 Datasets for "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics"
<h1><strong>Changes applied to V2</strong></h1> <p>In addition to the supplementary dataframes and AlphaFold models from each dataset in V1, V2 includes the additional data outlined below.</p> <p>The <strong>S2RCI</strong> and <strong>MD</strong> datasets include comprehensive analyses of AlphaFold2 models (both before and after truncation). These datasets feature: </p> <ul> <li><strong>AlphaFold2 Models</strong>: Both original and truncated structures. </li> <li><strong>WEBnma Modes</strong>: `modes.txt` files generated from WEBnma analysis, available for both non-truncated and truncated AF2 models. </li> <li><strong>Root-Mean-Square-Fluctuations (RMSF)</strong>: Profiles calculated before and after truncation of AF2 models. </li> <li><strong>NMR Data: Normal Mode Analysis (NMA)</strong>: Performed on corresponding NMR ensembles (see below). </li> </ul> <p> </p> <p>The <strong>NMR Data</strong> of NMA in these datasets includes: </p> <ul> <li>NMR ensembles </li> <li>Individual NMR models extracted from each ensemble </li> <li>STRIDE secondary structure calculations per-individual NMR models</li> <li>RMSF profiles per-individual NMR models</li> </ul> <p>For detailed information, please refer to the `Readme.txt` file within each corresponding folder. </p> <p>The <strong>S2 dataset</strong> includes all the features listed above, except for the NMR analysis.</p>
The dataset for the submitted paper " Time Series Analysis of Normal Mode Energetics for Rossby Wave Breaking and Saturation using a Simple Barotropic Model".
<p>These files are the data of the result in the submitted paper, titled "Time Series Analysis of Normal Mode Energetics for Rossby Wave Breaking and Saturation using a Simple Barotropic Model".</p> <ul> <li>File Description</li> </ul> <p>pv13.data : Exp. 1<br> pv17.data : Exp. 2</p> <p>The raw potential vorticity (PV) data for the Exp.1 and Exp.2, respectively, used in drawing the Fig.1, 2, and the supplemental movie 1 and 2.<br> These are the grid point value files, 72 levels for the zonal direction, 30 levels for meridional direction. More details are described in the next ctl files.</p> <p> </p> <p>pv13.ctl<br> pv17.ctl</p> <p>Description files for pv13.data and pv17.data. This will be called from grads_pv13.gs and grads_pv17.data, respectively.</p> <p>grads_pv13.gs<br> grads_pv17.gs</p> <p>GrADS script for mapping the PV.</p> <p> </p> <p>energy17.txt : Exp.2</p> <p>The time series table of energy values for exp.2.<br> One raw is identified by combination of the TIME in the experiment and zonal wave number N.</p>
Internal Normal Mode Analysis applied to RNA flexibility and conformational changes
<p>We investigated the capability of internal normal modes to reproduce RNA dynamics and predict observed RNA conformational changes, and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified rep- resentation of RNA structure and its potential energy. In this study, we considered three main data sets to investigate different aspects : i) one based on single-stranded RNA molecules for which all-atom MD simulations were computed; ii) one based on the available structures belonged to a specific Rfam family; iii) one based on the transition from unbound to bound RNA.</p> <p><strong>In each folder</strong></p> <p><em>modes.dat</em>: results obtained by iNMA (frequency and normal modes)</p> <p><em>das1.dat</em>: conversion from internal to cartesian normal modes</p> <p>Each file <em>name_enm.pdb</em> refers to a PDB structure with a CG representation (RNA three-bead model).</p> <p><strong>Dataset 1</strong>: d1.zip</p> <p>For the first dataset, we provide MD simulations converted into CG representation (RNA three-bead model), PCA analysis, the results obtained by iNMA for different values of distance cut-off <em>R</em><sub><em>c</em> </sub> and some scripts.</p> <p>Matlab and python scripts: </p> <p><em>analysis_pca.py</em>: to extract the different principal components</p> <p><em>analysis_PCA.m</em>: to compute overlap and cumative overlap in each folder</p> <p><em>analysis_complete_new.m</em>: to summarize the results</p> <p><strong>Dataset 2</strong>: d2.zip</p> <p>For this dataset, we provide the structure ensemble for Rfam family and the results obtained by iNMA for different values of distance cut-off <em>R</em><sub><em>c</em> </sub>and some scripts.</p> <p>PDB files:</p> <p><em>allensemble.pdb</em>: ensemble of PDB structures for a given Rfam family</p> <p><em>allensemble_enm.pdb</em>: ensemble of PDB structures for a given Rfam family converted to CG representation (RNA three-bead model)</p> <p><em>allensemble_enm_new.pdb</em>: ensemble of PDB structures for a given Rfam family with the same number of atoms for each model converted to CG representation (RNA three-bead model)</p> <p><em>model.pdb</em>: reference PDB structure</p> <p><em>model_enm.pdb</em>: reference PDB structure converted to CG representation (RNA three-bead model)</p> <p>Matlab script: </p> <p><em>pca_xray_anal.m</em>: PCA analysis, overlap, cumulative overlap, rmsip and plots</p> <p><strong>Dataset 3</strong>: d3.zip</p> <p>PDB structure:</p> <p><em>bound.pdb</em>: bound structure</p> <p><em>unbound.pdb</em>: unbound structure</p> <p><em>diff.dat</em>: difference between bound and unbound structure after superimposition </p> <p>RMSD<em>n </em>with n a number: the first column represents <span class="math-tex">\(\sqrt{\beta/2}\)</span></p> <p>Matlab script:</p> <p><em>rmsd_anal.m</em>: analysis best mode based on RMSD</p> <p><strong>Application to the CrPV-IRES</strong>: IRES.zip</p> <p>PDB structures:</p> <p> <em>IRES_cg.pdb</em>: Coarse-grain structure based on the PDB ID 5IT9</p> <p><em>b_end001_01_70.pdb</em>, <em>b_end001_01_80.pdb, b_end001_01_90.pdb</em>: Example of modified structures using the first lowest modes and different amplitudes <span class="math-tex">\(\beta\)</span></p> <p><em>b_end002_03_50.pdb</em>, <em>b_end002_03_60.pdb, b_end002_03_70.pdb</em>: Example of modified structures using the third lowest modes and different amplitudes <span class="math-tex">\(\beta\)</span></p>
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