| _version_ | 1866901478289965056 |
|---|---|
| author | Kolinski, Michal Puławski, Wojciech |
| author_facet | Kolinski, Michal Puławski, Wojciech |
| contents | <p>The repository contains supplementary info and the data acquired during the work on the publication entitled "Multiscale modeling of protofilament structures: A case study on insulin amyloid aggregates" and the scripts necessary to reproduce the results obtained in the work. This work was supported by the National Science Center of Poland (NCN), grant no. 2021/43/B/NZ2/02082.</p> <p> </p> <p><strong>INPUT_FILES </strong></p> <ul> <li><strong>Initial random conformations</strong>: <ul> <li>start_ins1.pdb, start_ins2.pdb: Examples of initial random conformations of insulin variants ins1 and ins2.</li> </ul> </li> <li><strong>CABSDOCK input files</strong>: <ul> <li>cabsdock_run.sh: Example input file for the CABSDOCK program.</li> <li>o a0.pdb, b0.pdb, ...: Input structures of random insulin conformations, split into separate chains.</li> <li>ca_rest: File containing CA (C-alpha) restraints for CABSDOCK.</li> <li>sc_rest: File containing SC (side-chain) restraints for CABSDOCK.</li> </ul> </li> </ul> <p><strong>PENTAMERS </strong></p> <ul> <li><strong>CG Procedure Results</strong>: <ul> <li>100 resulting models of coarse-grained (CG) simulations for insulin variants ins1 and ins2.</li> </ul> </li> </ul> <p><strong>RESULTING MODELS </strong></p> <ul> <li><strong>Best Scored Models</strong>: <ul> <li>model_best_scored.pdb: Best-scored model based on the <strong>pcaRMSD method</strong>.</li> <li>model_best_in_traj.pdb: Best model identified within the <strong>trajectory</strong>.</li> <li>model_best_in_top10.pdb: Best model within the <strong>top 10 scored models</strong> using the pcaRMSD method.</li> <li>model_best_in_top100.pdb: Best model within the <strong>top 100 scored models</strong> using the pcaRMSD method.</li> </ul> </li> </ul> <p><strong>SOFTWARE LINKS </strong></p> <ul> <li>Charmm https://www.academiccharmm.org/</li> <li>CabsDock https://bitbucket.org/lcbio/cabsdock/downloads/</li> <li>Rosetta https://docs.rosettacommons.org/docs/latest/Home</li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_14966161 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Multiscale modeling of protofilament structures: A case study on insulin amyloid aggregates Kolinski, Michal Puławski, Wojciech <p>The repository contains supplementary info and the data acquired during the work on the publication entitled "Multiscale modeling of protofilament structures: A case study on insulin amyloid aggregates" and the scripts necessary to reproduce the results obtained in the work. This work was supported by the National Science Center of Poland (NCN), grant no. 2021/43/B/NZ2/02082.</p> <p> </p> <p><strong>INPUT_FILES </strong></p> <ul> <li><strong>Initial random conformations</strong>: <ul> <li>start_ins1.pdb, start_ins2.pdb: Examples of initial random conformations of insulin variants ins1 and ins2.</li> </ul> </li> <li><strong>CABSDOCK input files</strong>: <ul> <li>cabsdock_run.sh: Example input file for the CABSDOCK program.</li> <li>o a0.pdb, b0.pdb, ...: Input structures of random insulin conformations, split into separate chains.</li> <li>ca_rest: File containing CA (C-alpha) restraints for CABSDOCK.</li> <li>sc_rest: File containing SC (side-chain) restraints for CABSDOCK.</li> </ul> </li> </ul> <p><strong>PENTAMERS </strong></p> <ul> <li><strong>CG Procedure Results</strong>: <ul> <li>100 resulting models of coarse-grained (CG) simulations for insulin variants ins1 and ins2.</li> </ul> </li> </ul> <p><strong>RESULTING MODELS </strong></p> <ul> <li><strong>Best Scored Models</strong>: <ul> <li>model_best_scored.pdb: Best-scored model based on the <strong>pcaRMSD method</strong>.</li> <li>model_best_in_traj.pdb: Best model identified within the <strong>trajectory</strong>.</li> <li>model_best_in_top10.pdb: Best model within the <strong>top 10 scored models</strong> using the pcaRMSD method.</li> <li>model_best_in_top100.pdb: Best model within the <strong>top 100 scored models</strong> using the pcaRMSD method.</li> </ul> </li> </ul> <p><strong>SOFTWARE LINKS </strong></p> <ul> <li>Charmm https://www.academiccharmm.org/</li> <li>CabsDock https://bitbucket.org/lcbio/cabsdock/downloads/</li> <li>Rosetta https://docs.rosettacommons.org/docs/latest/Home</li> </ul> |
| title | Multiscale modeling of protofilament structures: A case study on insulin amyloid aggregates |
| url | https://doi.org/10.5281/zenodo.14966161 |