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MD and QM/MM simulation dataset for "Enzymes can activate and mobilize dense biomolecular condensates across scales"

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Bibliographic Details
Main Authors:	Yagi, Kiyoshi, Ren, Weitong, Sugita, Yuji
Format:	Recurso digital
Published:	Zenodo 2026
Subjects:	molecular dynamics quantum mechanics / molecular mechanics enzyme reactions macromolecular crowding lactate dehydrogenase bovine serum albumin (BSA)
Online Access:	Acceder al recurso
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_version_	1866901616016228352
author	Yagi, Kiyoshi Ren, Weitong Sugita, Yuji
author_facet	Yagi, Kiyoshi Ren, Weitong Sugita, Yuji
contents	<h2>Directories of MD data</h2> <table> <tbody> <tr> <td>MD data</td> <td class="xl65">MD</td> </tr> <tr> <td>MD in 8 BSA of apo LDA (run1)</td> <td class="xl65">MD/apo_bsa8_1/</td> </tr> <tr> <td>MD in 8 BSA of apo LDA (run2)</td> <td class="xl65">MD/apo_bsa8_2/</td> </tr> <tr> <td>MD in 2 BSA of holo LDA (run1)</td> <td class="xl65">MD/holo_bsa2_1/</td> </tr> <tr> <td>MD in 2 BSA of holo LDA  (run2)</td> <td class="xl65">MD/holo_bsa2_2/</td> </tr> <tr> <td>MD in 4 BSA of holo LDA  (run1)</td> <td class="xl65">MD/holo_bsa4_1/</td> </tr> <tr> <td>MD in 4 BSA of holo LDA  (run2)</td> <td class="xl65">MD/holo_bsa4_2/</td> </tr> <tr> <td>MD in 4 BSA of holo LDA  (run3)</td> <td class="xl65">MD/holo_bsa4_3/</td> </tr> <tr> <td>MD in 8 BSA of holo LDA  (run1)</td> <td class="xl65">MD/holo_bsa8_1/</td> </tr> <tr> <td>MD in 8 BSA of holo LDA  (run2)</td> <td class="xl65">MD/holo_bsa8_2/</td> </tr> <tr> <td>ligands_diffusion in 8BSA of holo LDA (run1)</td> <td class="xl65">MD/ligands_diffusion_8bsa_1/</td> </tr> <tr> <td>ligands_diffusion in 8BSA of holo LDA (run1)</td> <td class="xl65">MD/ligands_diffusion_8bsa_2/</td> </tr> <tr> <td>MD in dilute condition of holo LDA (run1)</td> <td class="xl65">MD/dilute/holo/traj_1</td> </tr> <tr> <td>MD in dilute condition of holo LDA  (run2)</td> <td class="xl65">MD/dilute/holo/traj_2</td> </tr> <tr> <td>ligands diffusion in dilute condition (run1)</td> <td class="xl65">MD/dilute/apo/ligand_diffusion_1/</td> </tr> <tr> <td>ligands diffusion in dilute condition (run2)</td> <td class="xl65">MD/dilute/apo/ligand_diffusion_2/</td> </tr> </tbody> </table> <p> </p> <h2>Directories of QM/MM data</h2> <table> <tbody> <tr> <td>QM/MM data</td> <td class="xl65">QMMM_3h3f_amber</td> </tr> <tr> <td>QM/MM OPT (closed state)</td> <td class="xl65">QMMM_3h3f_amber/3.qmmm1c_mep</td> </tr> <tr> <td>QM/MM MEP (closed state)</td> <td class="xl65">QMMM_3h3f_amber/4.qmmm1c_mep</td> </tr> <tr> <td>QM/MM US (closed state)</td> <td class="xl65">QMMM_3h3f_amber/5.qmmm1c_us</td> </tr> <tr> <td>QM/MM OPT (open state)</td> <td class="xl65">QMMM_3h3f_amber/3.qmmm1o_mep</td> </tr> <tr> <td>QM/MM MEP (open state)</td> <td class="xl65">QMMM_3h3f_amber/4.qmmm1o_mep</td> </tr> <tr> <td>QM/MM US (open state)</td> <td class="xl65">QMMM_3h3f_amber/5.qmmm1o_us</td> </tr> </tbody> </table> <p> </p> <h2>Data of Figures in the paper</h2> <table> <tbody> <tr> <td>Figure</td> <td>figure_data</td> </tr> </tbody> </table> <p> </p>
format	Recurso digital
id	zenodo_https___doi_org_10_5281_zenodo_19548047
institution	Zenodo
language
publishDate	2026
publisher	Zenodo
record_format	zenodo
spellingShingle	MD and QM/MM simulation dataset for "Enzymes can activate and mobilize dense biomolecular condensates across scales" Yagi, Kiyoshi Ren, Weitong Sugita, Yuji molecular dynamics quantum mechanics / molecular mechanics enzyme reactions macromolecular crowding lactate dehydrogenase bovine serum albumin (BSA) <h2>Directories of MD data</h2> <table> <tbody> <tr> <td>MD data</td> <td class="xl65">MD</td> </tr> <tr> <td>MD in 8 BSA of apo LDA (run1)</td> <td class="xl65">MD/apo_bsa8_1/</td> </tr> <tr> <td>MD in 8 BSA of apo LDA (run2)</td> <td class="xl65">MD/apo_bsa8_2/</td> </tr> <tr> <td>MD in 2 BSA of holo LDA (run1)</td> <td class="xl65">MD/holo_bsa2_1/</td> </tr> <tr> <td>MD in 2 BSA of holo LDA  (run2)</td> <td class="xl65">MD/holo_bsa2_2/</td> </tr> <tr> <td>MD in 4 BSA of holo LDA  (run1)</td> <td class="xl65">MD/holo_bsa4_1/</td> </tr> <tr> <td>MD in 4 BSA of holo LDA  (run2)</td> <td class="xl65">MD/holo_bsa4_2/</td> </tr> <tr> <td>MD in 4 BSA of holo LDA  (run3)</td> <td class="xl65">MD/holo_bsa4_3/</td> </tr> <tr> <td>MD in 8 BSA of holo LDA  (run1)</td> <td class="xl65">MD/holo_bsa8_1/</td> </tr> <tr> <td>MD in 8 BSA of holo LDA  (run2)</td> <td class="xl65">MD/holo_bsa8_2/</td> </tr> <tr> <td>ligands_diffusion in 8BSA of holo LDA (run1)</td> <td class="xl65">MD/ligands_diffusion_8bsa_1/</td> </tr> <tr> <td>ligands_diffusion in 8BSA of holo LDA (run1)</td> <td class="xl65">MD/ligands_diffusion_8bsa_2/</td> </tr> <tr> <td>MD in dilute condition of holo LDA (run1)</td> <td class="xl65">MD/dilute/holo/traj_1</td> </tr> <tr> <td>MD in dilute condition of holo LDA  (run2)</td> <td class="xl65">MD/dilute/holo/traj_2</td> </tr> <tr> <td>ligands diffusion in dilute condition (run1)</td> <td class="xl65">MD/dilute/apo/ligand_diffusion_1/</td> </tr> <tr> <td>ligands diffusion in dilute condition (run2)</td> <td class="xl65">MD/dilute/apo/ligand_diffusion_2/</td> </tr> </tbody> </table> <p> </p> <h2>Directories of QM/MM data</h2> <table> <tbody> <tr> <td>QM/MM data</td> <td class="xl65">QMMM_3h3f_amber</td> </tr> <tr> <td>QM/MM OPT (closed state)</td> <td class="xl65">QMMM_3h3f_amber/3.qmmm1c_mep</td> </tr> <tr> <td>QM/MM MEP (closed state)</td> <td class="xl65">QMMM_3h3f_amber/4.qmmm1c_mep</td> </tr> <tr> <td>QM/MM US (closed state)</td> <td class="xl65">QMMM_3h3f_amber/5.qmmm1c_us</td> </tr> <tr> <td>QM/MM OPT (open state)</td> <td class="xl65">QMMM_3h3f_amber/3.qmmm1o_mep</td> </tr> <tr> <td>QM/MM MEP (open state)</td> <td class="xl65">QMMM_3h3f_amber/4.qmmm1o_mep</td> </tr> <tr> <td>QM/MM US (open state)</td> <td class="xl65">QMMM_3h3f_amber/5.qmmm1o_us</td> </tr> </tbody> </table> <p> </p> <h2>Data of Figures in the paper</h2> <table> <tbody> <tr> <td>Figure</td> <td>figure_data</td> </tr> </tbody> </table> <p> </p>
title	MD and QM/MM simulation dataset for "Enzymes can activate and mobilize dense biomolecular condensates across scales"
topic	molecular dynamics quantum mechanics / molecular mechanics enzyme reactions macromolecular crowding lactate dehydrogenase bovine serum albumin (BSA)
url	https://doi.org/10.5281/zenodo.19548047