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2025
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| Acceso en línea: | https://doi.org/10.5281/zenodo.14861195 |
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| _version_ | 1866902072631230464 |
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| author | Granja, Ana Clara Chagas, Marcelo Rocha, Willian Aglas, Lorenz Ferreira, Fatima Valente, Ana Paula Moraes, Adolfo |
| author_facet | Granja, Ana Clara Chagas, Marcelo Rocha, Willian Aglas, Lorenz Ferreira, Fatima Valente, Ana Paula Moraes, Adolfo |
| contents | <p>The zip files contain data related to individual molecular dynamics simulations. The contents of each archive are as follows:<br><br>*archive*.pdb -> Initial Structure<br>*archive*_solv.pdb -> Start Structure (Solvated) <br>*archive*.prmtop -> Initial Topology *archive*.inpcrd -> Initial Velocities<br>*archive*.mdcrd -> Representative Trajectory File Min.in -> Input for First Minimization Min-II.in -> Input for Seccond Minimization</p> <p>stage1_heat_5_50K_for_10ps.in -> Input for Heating from 5K to 50K in 10 ps<br>stage1.rst -> Restart Heating from 5K to 50K in 10 ps<br>stage1.out -> Log for Heating from 5K to 50K in 10 ps<br>stage1.mdcrd -> Trajectory of Heating from 5K to 50K in 10 ps</p> <p>stage1_equil_50K_for_100ps.in -> Equilibration in 50K for 100 ps<br>stage2.rst -> Restart Equilibration in 50K for 100 ps<br>stage2.out -> Log for Equilibration in 50K for 100 ps<br>stage2.mdcrd -> Trajectory of Equilibration in 50K for 100 ps</p> <p>stage2_heat_50_100K_for_10ps.in -> Input for Heating from 50K to 100K in 10 ps<br>stage3.rst -> Restart Heating from 50K to 100K in 10 ps<br>stage3.out -> Log for Heating from 50K to 100K in 10 ps<br>stage3.mdcrd -> Trajectory of Heating from 50K to 100K in 10 ps</p> <p>stage2_equil_100K_for_100ps.in -> Input for Equilibration in 100K for 100 ps<br>stage4.rst -> Restart Equilibration in 100K for 100 ps<br>stage4.out -> Log for Equilibration in 100K for 100 ps<br>stage4.mdcrd -> Trajectory of Equilibration in 100K for 100 ps</p> <p>stage3_heat_100_150K_for_10ps.in -> Input for Heating from 100K to 150K in 10 ps<br>stage5.rst -> Restart Heating from 50K to 100K in 10 ps<br>stage5.out -> Log for Heating from 50K to 100K in 10 ps<br>stage5.mdcrd -> Trajectory of Heating from 50K to 100K in 10 ps</p> <p>stage3_equil_150K_for_100ps.in -> Input for Equilibration in 150K for 100 ps<br>stage6.rst -> Restart Equilibration in 150K for 100 ps<br>stage6.out -> Log for Equilibration in 150K for 100 ps<br>stage6.mdcrd -> Trajectory of Equilibration in 150K for 100 ps</p> <p>stage4_heat_150_200K_for_10ps.in -> Input for Heating from 150K to 200K in 10 ps<br>stage7.rst -> Restart Heating from 150K to 200K in 10 ps<br>stage7.out -> Log for Heating from 150K to 200K in 10 ps<br>stage7.mdcrd -> Trajectory of Heating from 150K to 200K in 10 ps</p> <p>stage4_equil_200K_for_100ps.in -> Input for Equilibration in 200K for 100 ps<br>stage8.rst -> Restart Equilibration in 200K for 100 ps<br>stage8.out -> Log for Equilibration in 200K for 100 ps<br>stage8.mdcrd -> Trajectory of Equilibration in 200K for 100 ps</p> <p>stage5_heat_200_250K_for_10ps.in -> Input for Heating from 200K to 250K in 10 ps<br>stage9.rst -> Restart Heating from 200K to 250K in 10 ps<br>stage9.out -> Log for Heating from 200K to 250K in 10 ps<br>stage9.mdcrd -> Trajectory of Heating from 200K to 250K in 10 ps</p> <p>stage5_equil_250K_for_100ps.in -> Input for Equilibration in 250K for 100 ps<br>stage10.rst -> Restart Equilibration in 250K for 100 ps<br>stage10.out -> Log for Equilibration in 250K for 100 ps<br>stage10.mdcrd -> Trajectory of Equilibration in 250K for 100 ps</p> <p>stage6_heat_250_300K_for_10ps.in -> Input for Heating from 250K to 300K in 10 ps<br>stage11.rst -> Restart Heating from 250K to 300K in 10 ps<br>stage11.out -> Log for Heating from 250K to 300K in 10 ps<br>stage11.mdcrd -> Trajectory of Heating from 250K to 300K in 10 ps</p> <p>stage6_equil_300K_for_5000ps.in -> Input for Equilibration in 300K for 5000 ps<br>stage12.rst -> Restart Equilibration in 300K for 5000 ps<br>stage12.out -> Log for Equilibration in 300K for 5000 ps<br>stage12.mdcrd -> Trajectory of Equilibration in 300K for 5000 ps</p> <p>Prod.in -> Input for Step for Production (2 ns)</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_14861195 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Conformational Plasticity of β-rich Proteins: Molecular Insights into Stability, Dynamics, and Functional Adaptation of Bet v 1-like Proteins Granja, Ana Clara Chagas, Marcelo Rocha, Willian Aglas, Lorenz Ferreira, Fatima Valente, Ana Paula Moraes, Adolfo <p>The zip files contain data related to individual molecular dynamics simulations. The contents of each archive are as follows:<br><br>*archive*.pdb -> Initial Structure<br>*archive*_solv.pdb -> Start Structure (Solvated) <br>*archive*.prmtop -> Initial Topology *archive*.inpcrd -> Initial Velocities<br>*archive*.mdcrd -> Representative Trajectory File Min.in -> Input for First Minimization Min-II.in -> Input for Seccond Minimization</p> <p>stage1_heat_5_50K_for_10ps.in -> Input for Heating from 5K to 50K in 10 ps<br>stage1.rst -> Restart Heating from 5K to 50K in 10 ps<br>stage1.out -> Log for Heating from 5K to 50K in 10 ps<br>stage1.mdcrd -> Trajectory of Heating from 5K to 50K in 10 ps</p> <p>stage1_equil_50K_for_100ps.in -> Equilibration in 50K for 100 ps<br>stage2.rst -> Restart Equilibration in 50K for 100 ps<br>stage2.out -> Log for Equilibration in 50K for 100 ps<br>stage2.mdcrd -> Trajectory of Equilibration in 50K for 100 ps</p> <p>stage2_heat_50_100K_for_10ps.in -> Input for Heating from 50K to 100K in 10 ps<br>stage3.rst -> Restart Heating from 50K to 100K in 10 ps<br>stage3.out -> Log for Heating from 50K to 100K in 10 ps<br>stage3.mdcrd -> Trajectory of Heating from 50K to 100K in 10 ps</p> <p>stage2_equil_100K_for_100ps.in -> Input for Equilibration in 100K for 100 ps<br>stage4.rst -> Restart Equilibration in 100K for 100 ps<br>stage4.out -> Log for Equilibration in 100K for 100 ps<br>stage4.mdcrd -> Trajectory of Equilibration in 100K for 100 ps</p> <p>stage3_heat_100_150K_for_10ps.in -> Input for Heating from 100K to 150K in 10 ps<br>stage5.rst -> Restart Heating from 50K to 100K in 10 ps<br>stage5.out -> Log for Heating from 50K to 100K in 10 ps<br>stage5.mdcrd -> Trajectory of Heating from 50K to 100K in 10 ps</p> <p>stage3_equil_150K_for_100ps.in -> Input for Equilibration in 150K for 100 ps<br>stage6.rst -> Restart Equilibration in 150K for 100 ps<br>stage6.out -> Log for Equilibration in 150K for 100 ps<br>stage6.mdcrd -> Trajectory of Equilibration in 150K for 100 ps</p> <p>stage4_heat_150_200K_for_10ps.in -> Input for Heating from 150K to 200K in 10 ps<br>stage7.rst -> Restart Heating from 150K to 200K in 10 ps<br>stage7.out -> Log for Heating from 150K to 200K in 10 ps<br>stage7.mdcrd -> Trajectory of Heating from 150K to 200K in 10 ps</p> <p>stage4_equil_200K_for_100ps.in -> Input for Equilibration in 200K for 100 ps<br>stage8.rst -> Restart Equilibration in 200K for 100 ps<br>stage8.out -> Log for Equilibration in 200K for 100 ps<br>stage8.mdcrd -> Trajectory of Equilibration in 200K for 100 ps</p> <p>stage5_heat_200_250K_for_10ps.in -> Input for Heating from 200K to 250K in 10 ps<br>stage9.rst -> Restart Heating from 200K to 250K in 10 ps<br>stage9.out -> Log for Heating from 200K to 250K in 10 ps<br>stage9.mdcrd -> Trajectory of Heating from 200K to 250K in 10 ps</p> <p>stage5_equil_250K_for_100ps.in -> Input for Equilibration in 250K for 100 ps<br>stage10.rst -> Restart Equilibration in 250K for 100 ps<br>stage10.out -> Log for Equilibration in 250K for 100 ps<br>stage10.mdcrd -> Trajectory of Equilibration in 250K for 100 ps</p> <p>stage6_heat_250_300K_for_10ps.in -> Input for Heating from 250K to 300K in 10 ps<br>stage11.rst -> Restart Heating from 250K to 300K in 10 ps<br>stage11.out -> Log for Heating from 250K to 300K in 10 ps<br>stage11.mdcrd -> Trajectory of Heating from 250K to 300K in 10 ps</p> <p>stage6_equil_300K_for_5000ps.in -> Input for Equilibration in 300K for 5000 ps<br>stage12.rst -> Restart Equilibration in 300K for 5000 ps<br>stage12.out -> Log for Equilibration in 300K for 5000 ps<br>stage12.mdcrd -> Trajectory of Equilibration in 300K for 5000 ps</p> <p>Prod.in -> Input for Step for Production (2 ns)</p> |
| title | Conformational Plasticity of β-rich Proteins: Molecular Insights into Stability, Dynamics, and Functional Adaptation of Bet v 1-like Proteins |
| url | https://doi.org/10.5281/zenodo.14861195 |