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8 results for “molecular flexibility”

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zenodo40/100

How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study

<p>The data necessary to independently reproduce the MD simulations and the first part of the simulation trajectories reported in the paper "<strong>How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study</strong>", by Lemmens et al.</p> <p>Due to Zenodo data deposition limits, every 10th frame of the MD simulation trajectories is included. Due to Zenodo deposition limits, MD trajectory files for this paper are also available at 10.5281/zenodo.14260246.</p>

opencc-by-4.0Oct 2024View details →
zenodo36/100

Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

<p>Ocean warming favors pelagic tunicates, such as salps, that exhibit increasingly frequent and rapid population blooms, impacting trophic dynamics and composition and human marine-dependent activities. Salp blooms are a result of their successful reproductive life history, alternating seasonally between asexual and sexual protogynous (i.e. sequential) hermaphroditic stages. While predicting future salp bloom frequency and intensity relies on an understanding of the transitions during the sexual stage from female through parturition and subsequent sex change to male, these transitions have not been explored at the molecular level. Here we report the development of the first complete genome of S. thompsoni and the North Atlantic sister species S. aspera. Genome and comparative analyses reveal an abundance of repeats and G-quadruplex (G4) motifs, a highly stable secondary structure, distributed throughout both salp genomes, a feature shared with other tunicates that perform alternating sexual-asexual reproductive strategies. Transcriptional analyses across sexual reproductive stages for S. thompsoni revealed genes associated with male sex differentiation and spermatogenesis are expressed as early as birth and before parturition, inconsistent with previous descriptions of sequential sexual differentiation in salps. Our findings suggest salp are poised for reproductive success at birth, increasing the potential for bloom formation as ocean temperatures rise.</p>

opencc-by-4.0Nov 2023View details →
zenodo36/100

FEater dataset: A molecular fragment dataset to benchmark the robustness of 3D flexible object recognition

<p>This dataset is associated with the work: Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models</p> <pre><code># Original FEater-Single and FEater_Dual dataset. FEater_Single ├── TestSet_coord.h5 ├── TrainingSet_coord.h5 └── ValidationSet_coord.h5 FEater_Dual ├── TestSet_coord.h5 ├── TrainingSet_coord.h5 └── ValidationSet_coord.h5 # Non-redundant baseline dataset FEater_Baseline ├── TestSet_Dual.h5 ├── TestSet_Single.h5 ├── TrainingSet_Dual.h5 └── TrainingSet_Single.h5 # FEater-Single and FEater_Dual in different sample size FEater_Mini200 ├── Mini200_Dual.h5 └── Mini200_Single.h5 FEater_Mini400 ├── Mini400_Dual.h5 └── Mini400_Single.h5 FEater_Mini800 ├── Mini800_Dual.h5 └── Mini800_Single.h5</code></pre> <p>For further details of the usage, please visit the original GitHub repository:&nbsp;<a title="FEater_repo" href="https://github.com/miemiemmmm/FEater" target="_blank" rel="noopener">https://github.com/miemiemmmm/FEater</a></p>

opencc-by-4.0Nov 2024View details →
zenodo36/100

How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study - Second part

<p>Second part of the data deposition for the paper "<strong>How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study</strong>", by Lemmens et al. Part one is availible via <a href="https://doi.org/10.5281/zenodo.13929049">10.5281/zenodo.13929049</a></p>

opencc-by-4.0Dec 2024View details →
zenodo36/100

Somatic hypermutation-mediated paratope flexibility improves the cross-reactivity of human malaria antibodies -- Molecular Dynamics dataset

<p>4493 Manuscript Data<br>====================</p> <p>author: Anton Hanke<br>size of uncompressed folder: ~19Gb.<br>DOI: 10.5281/zenodo.11470585</p> <p># Standard MD simulation data</p> <p>Standard Simulations were generated with gromacs 2021.5 using the charmm36m forcefield Juli 2021 release tarball (https://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2021.ff.tgz).<br>Post processed (PBC) simulations are structured as follows:<br>Mature generally refers to the wildtype 4493 antibody.</p> <p>- simulations/standardMD<br>&nbsp; |<br>&nbsp; |- prod.mdp &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;example production mdp file used to run all production simulations.<br>&nbsp; |<br>&nbsp; |- mature &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Mature simulation set. (folder and file naming the same in all simulation directories)<br>&nbsp; | &nbsp;|- {peptide}_{replicate}_prod.gro &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; {peptide} = peptide; {replicate} = standard MD replicate<br>&nbsp; | &nbsp;|- {peptide}_{replicate}_prod.tpr<br>&nbsp; | &nbsp;`- {peptide}_{replicate}_prod_align_noPBC.xtc (10Frames/ns)<br>&nbsp; |<br>&nbsp; |- mature_rerun &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Additional set of replicates with the wildtype 4493.<br>&nbsp; |- matureCapped &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Set of simulations with termini capped peptides<br>&nbsp; |- mature_nanpv2 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Set of simulations with NPDP similar positioning of NANP<br>&nbsp; |- wo_pep &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Set of simulations without peptides for germline and mature<br>&nbsp; `- germline &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Set of germline simulations.</p> <p><br># RAMD simulation data</p> <p>RAMD simulations were generated with gromacs_2020.5 patched with RAMDv2 modified to account for the connected multiple ligand groups.<br>(Source code provided as tar file ./sw/gromacs_ramd_patchv2.tar.gz)</p> <p>Not all trajectories contain an unbinding event (gromacs CUDA bug.).&nbsp;<br>These trajectories were not considered in the analysis of simulations.&nbsp;</p> <p>- simulations/ramd<br>&nbsp; |<br>&nbsp; |- prod.mdp &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Exemplary production mdp file with RAMD settings, these were used in all trajectories w/<br>&nbsp; | &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; differing RAMD random seed.<br>&nbsp; |<br>&nbsp; |- mature_2.625kcalmolA_4.0_3.0<br>&nbsp; | &nbsp;|- {peptide}_{replicate}_prod_{startFrame}.gro &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; {peptide} = peptide; {replicate} = standard MD replicate; {startFrame} = Frame in standard MD used to start simulation.<br>&nbsp; | &nbsp;|- {peptide}_{replicate}_prod_{startFrame}.tpr<br>&nbsp; | &nbsp;|- {peptide}_{replicate}_prod_{startFrame}.ndx<br>&nbsp; | &nbsp;|- {peptide}_{replicate}_prod_{startFrame}_align_noPBC.xtc &nbsp; &nbsp; &nbsp; (100Frames/ns) Files omited due to size -- available on request.<br>&nbsp; | &nbsp;`- {peptide}_{replicate}_prod_{startFrame}_lastframe.pdb &nbsp; &nbsp; &nbsp; &nbsp; Last frame of the processed RAMD trajectory.<br>&nbsp; `- gl_2.625kcalmolA_4.0_3.0</p> <p><br># Analysis</p> <p>- analysis<br>&nbsp; |<br>&nbsp; |- entropie &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Quasi harmonic entropy estimation.<br>&nbsp; | &nbsp;|- inp &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Concatenated &amp; Bootstrapped, coarse-grained and aligned trajectories of all systems<br>&nbsp; | &nbsp;|- out &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; CPPTRAJ runs to calculate QHE on the bootstrapped trajectories<br>&nbsp; | &nbsp;|- run_complex.sh &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Script running analysis.<br>&nbsp; | &nbsp;|- ana.py &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Script to calculte average and std of QHE for each system. (generates *.out *.tsv *.png)<br>&nbsp; | &nbsp;|- cg.py &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Script used to bootstrap, coarse-grain align and build average structure with.<br>&nbsp; | &nbsp;`- delta_entropies.ods &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Excel file used to calculate Tab 1. in Main text of paper from entropies.out.<br>&nbsp; |<br>&nbsp; |- mmpbsa &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MMPBSA calculations (MM + SolvEnergy) with gmx_MMPBSA<br>&nbsp; | &nbsp;|- inp &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Input trajectories and topologies processed for MMPBSA<br>&nbsp; | &nbsp;|- out/gmx_mmpbsa &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Output directories in which gmx_MMPBSA was run.<br>&nbsp; | &nbsp;| &nbsp;` *.dat &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Output files containing calculated energy terms from gmx_MMPBSA.<br>&nbsp; | &nbsp;|- mmpbsa.in &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MMPBSA input file used to run analysis.<br>&nbsp; | &nbsp;|- plot_results.py &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Python script to plot correlation of MMPBSA output with experimental data<br>&nbsp; | &nbsp;|- pca_eig_extr.py &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Script to reduce simulations to regions of high probability density within trajectory (not used in the present analysis)<br>&nbsp; | &nbsp;|- slurm-91315023.out &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Log file of the analysis run<br>&nbsp; | &nbsp;`- run_mmpbsa.sh &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Shell script to run the MMPBSA analysis (generates input and output file trees).<br>&nbsp; |<br>&nbsp; `- ramd &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; RAMD analysation.<br>&nbsp; &nbsp; &nbsp;|- run.sh &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Shell script to run the analysis<br>&nbsp; &nbsp; &nbsp;|- run_ramd_ana.py &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Python script called by `run.sh` to run the analysis using `ramdAnalysis.py`<br>&nbsp; &nbsp; &nbsp;|- contact_clusters.py &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Python script to generate plots based on output of the analysis.<br>&nbsp; &nbsp; &nbsp;|- ramdAnalysis.py &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Python module containing analysis classes called/used within `run_ramd_ana.py`<br>&nbsp; &nbsp; &nbsp;| &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Based on tauRAMD &amp; Fingerprint analysis by Dr. Daria Khokh (https://doi.org/10.1021%2Facs.jctc.8b00230; https://doi.org/10.1063%2F5.0019088)<br>&nbsp; &nbsp; &nbsp;|- abrun.* &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Log files from the present run<br>&nbsp; &nbsp; &nbsp;|- *.svg; *.png &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Analysis output files.<br>&nbsp; &nbsp; &nbsp;|- tramd_patchv2/ &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Output PDB structures from the analysis (excluded due to size, available on request)<br>&nbsp; &nbsp; &nbsp;`- representatives.pse &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Pymol session of cluster representatives along unbinding for germline and wildtype with contact probabilities within the<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; cluster mapped as b-factor.</p> <p># Figures</p> <p>- figure_pdbs &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; PDB files (and pymol sessions) used to generate figures in the papers main text.</p>

opencc-by-4.0Jul 2024View details →
zenodo36/100

Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"

<p>The tar file&nbsp;contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making.</p> <p>All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 &Aring; for ADK and 1.8 and 3 &Aring; for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow.</p> <p>The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a></p> <p>The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a></p> <p>To obtain maximum compression of the data, the tar command used to generate this tarball was:</p> <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre> <p>&nbsp;</p>

opencc-by-4.0Mar 2023View details →
zenodo32/100

Supporting data for Absorbing stress via molecular crumple zones: Strain engineering flexibility into the rigid UiO-66 material

<p>Supplementary data containing relevant structural information for the manuscript &#39;Absorbing stress via molecular crumple zones: Strain engineering&nbsp; flexibility into the rigid UiO-66 material&#39;.</p> <p>Please also refer to https://github.com/SvenRogge/supporting-info for additional input scripts to reproduce these results and a detailed description of the different files.</p>

opencc-by-4.0Jan 2023View details →
zenodo28/100

ApoDock: Ligand-Conditioned Sidechain Packing for Flexible Molecular Docking

Open the record for dataset details and reuse information.

opencc-by-4.0Nov 2024View details →

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