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3 results for “molecular forecaster”
FORECASTING MOLECULAR DYNAMICS SIMULATIONS OF POLYMER-LIPIDS IN SOLUTION WITH RNNs
<p>Files and scripts pertaining to our work: </p> <ul> <li>GROMACS files for the topology (DSPE+PEG.top) and the initial structure of the aggregate (DSPE+PEG_EA_NPT.gro)</li> <li>GROMACS topology file for the ethyl acetate molecule: EA_SI.top</li> <li>Scripts to submit the <em>GROMACS</em> utilities for calculation of the interaction energies are described in README.txt (Subset_energy.sh , Interaction_energies.sh)</li> <li>Scripts pertaining to <em>PyTorch</em> use and access of methods are described in README.txt (Multiple-run.sh. Job.sh, Pytorch_train-model.py)</li> <li>Scripts pertaining to <em>scikit learn </em>access for the Expectation Maximization clustering are described in the README.txt (Job_EM.sh, EM_Clustering.py)</li> <li>Files with the time series of the potential energy (PE) and interaction energy (IE) of the DSPE-PEG aggregate with the ethyl acetate solvent. Series contain 500,000 snapshots taken every 10 fs along the NVT Molecular Dynamics trajectory at 300 K and 906.3 kg/m<sup>3</sup> density. The molecular solution is in a cubic box of edge length 13.76 nm, containing 16,000 ethyl acetate molecules and one aggregate of 4 DSPE-PEG-amide macromolecules (224,000 atoms): Data_Andrews_etal_DSPE-PEG_2022.zip</li> <li>ArXiv preprint: https://doi.org/10.48550/arXiv.2203.00151 (JAndrews_etal_arXiv-doi.pdf)</li> </ul>
Virtual Screening with Molecular Forecaster
<p>Commercially available compounds for USP5 zinc-finger ubiquitin binding domain (ZnF-UBD) were identified with Molecular Forecasters (MFI) FITTED docking platform. Preliminary assessment of docking for USP5 ZnF-UBD with FITTED can be found <a href="https://zenodo.org/record/2620208#.XQO2pYhKjIV">here</a>.</p>
Molecular Forecaster Inc (MFI): USP5 Zf-UBD
<p>Self-docking of ligands in USP5 zinc finger ubiquitin binding domain (Zf-UBD) co-crystal structures using the Forecaster FITTED docking platform is assessed and the ranking success of FITTED rigid protein docking vs. MATCHUP flexible protein docking on a library of experimentally tested compounds is investigated. </p>
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OpenNeuro
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