https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2023Terashi_DeepMainMast 2026-05-24T20:20:46Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2023Terashi_DeepMainMast&diff=4529&oldid=prev 2024-01-10T08:12:35Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 08:12, 10 January 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Citation ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Citation ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Cheng</del>, <del style="font-weight: bold; text-decoration: none;">Yuanhao </del>/ <del style="font-weight: bold; text-decoration: none;">Huang</del>, <del style="font-weight: bold; text-decoration: none;">Xiaojun </del>/ <del style="font-weight: bold; text-decoration: none;">Xu</del>, <del style="font-weight: bold; text-decoration: none;">Bin </del>/ <del style="font-weight: bold; text-decoration: none;">Ding</del>, <del style="font-weight: bold; text-decoration: none;">Wei</del>. <del style="font-weight: bold; text-decoration: none;">AutoEMage</del>: <del style="font-weight: bold; text-decoration: none;">automatic data transfer, preprocessing, real-time display and monitoring in </del>cryo-EM. 2023. <del style="font-weight: bold; text-decoration: none;">J. Applied Crystallography, Vol. 56, No. 6</del>, p. <del style="font-weight: bold; text-decoration: none;">1865</del>-<del style="font-weight: bold; text-decoration: none;">1873 </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Terashi</ins>, <ins style="font-weight: bold; text-decoration: none;">Genki </ins>/ <ins style="font-weight: bold; text-decoration: none;">Wang</ins>, <ins style="font-weight: bold; text-decoration: none;">Xiao </ins>/ <ins style="font-weight: bold; text-decoration: none;">Prasad</ins>, <ins style="font-weight: bold; text-decoration: none;">Devashish </ins>/ <ins style="font-weight: bold; text-decoration: none;">Nakamura</ins>, <ins style="font-weight: bold; text-decoration: none;">Tsukasa / Kihara, Daisuke</ins>. <ins style="font-weight: bold; text-decoration: none;">DeepMainmast</ins>: <ins style="font-weight: bold; text-decoration: none;">integrated protocol of protein structure modeling for </ins>cryo-EM <ins style="font-weight: bold; text-decoration: none;">with deep learning and structure prediction</ins>. 2023. <ins style="font-weight: bold; text-decoration: none;">Nature Methods</ins>, p. <ins style="font-weight: bold; text-decoration: none;">1</ins>-<ins style="font-weight: bold; text-decoration: none;">10 </ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Abstract ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Abstract ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Cryo</del>-electron microscopy <del style="font-weight: bold; text-decoration: none;">(cryo-EM)</del>, <del style="font-weight: bold; text-decoration: none;">especially single-particle analysis</del>, <del style="font-weight: bold; text-decoration: none;">has</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Three</ins>-<ins style="font-weight: bold; text-decoration: none;">dimensional structure modeling from maps is an indispensable</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">become </del>a <del style="font-weight: bold; text-decoration: none;">powerful technique for visualizing the </del>structure <del style="font-weight: bold; text-decoration: none;">of biological</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">step for studying proteins and their complexes with cryogenic electron</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">macromolecules at high resolution. However</del>, <del style="font-weight: bold; text-decoration: none;">data acquisition in cryo-EM is</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">microscopy. Although the resolution of determined cryogenic </ins>electron</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">time consuming because it requires the collection </del>of <del style="font-weight: bold; text-decoration: none;">thousands of images </del>to</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>microscopy <ins style="font-weight: bold; text-decoration: none;">maps has generally improved</ins>, <ins style="font-weight: bold; text-decoration: none;">there are still many cases where</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">achieve a high</del>-<del style="font-weight: bold; text-decoration: none;">quality reconstruction</del>. <del style="font-weight: bold; text-decoration: none;">Real-time preprocessing and display of</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">tracing protein main chains is difficult</ins>, <ins style="font-weight: bold; text-decoration: none;">even in maps determined at a</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>the <del style="font-weight: bold; text-decoration: none;">images can greatly enhance the efficiency </del>and <del style="font-weight: bold; text-decoration: none;">quality of data collection</del>. <del style="font-weight: bold; text-decoration: none;">This</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">near-atomic resolution. Here we developed </ins>a <ins style="font-weight: bold; text-decoration: none;">protein </ins>structure <ins style="font-weight: bold; text-decoration: none;">modeling</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">study presents AutoEMage</del>, <del style="font-weight: bold; text-decoration: none;">a new open-source software package that automates</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">method, DeepMainmast</ins>, <ins style="font-weight: bold; text-decoration: none;">which employs deep learning to capture the</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">data transfer, preprocessing and real-time display in cryo-EM experiments.</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">local map features </ins>of <ins style="font-weight: bold; text-decoration: none;">amino acids and atoms </ins>to <ins style="font-weight: bold; text-decoration: none;">assist main</ins>-<ins style="font-weight: bold; text-decoration: none;">chain tracing</ins>.</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">AutoEMage also includes a real</del>-<del style="font-weight: bold; text-decoration: none;">time data monitoring system that alerts users to</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Moreover, we integrated AlphaFold2 with </ins>the <ins style="font-weight: bold; text-decoration: none;">de novo density tracing</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">issues with their data</del>, <del style="font-weight: bold; text-decoration: none;">allowing them to take corrective actions accordingly. The</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">protocol to combine their complementary strengths </ins>and <ins style="font-weight: bold; text-decoration: none;">achieved even</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">software </del>is <del style="font-weight: bold; text-decoration: none;">equipped with an easy-to-use graphical user interface that provides</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">higher accuracy than each method alone</ins>. <ins style="font-weight: bold; text-decoration: none;">Additionally</ins>, <ins style="font-weight: bold; text-decoration: none;">the protocol is</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">seamless data screening and real-time feedback on data quality and microscope</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">able to accurately assign the chain identity to the structure models of</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">status</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">homo</ins>-<ins style="font-weight: bold; text-decoration: none;">multimers</ins>, <ins style="font-weight: bold; text-decoration: none;">which </ins>is <ins style="font-weight: bold; text-decoration: none;">not a trivial task for existing methods</ins>.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Keywords ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Keywords ==</div></td></tr> </table>

WikiSysop https://3demmethods.i2pc.es/index.php?title=2023Terashi_DeepMainMast&diff=4528&oldid=prev 2024-01-10T08:05:48Z

<p>Created page with &quot;== Citation == Cheng, Yuanhao / Huang, Xiaojun / Xu, Bin / Ding, Wei. AutoEMage: automatic data transfer, preprocessing, real-time display and monitoring in cryo-EM. 2023. J....&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Cheng, Yuanhao / Huang, Xiaojun / Xu, Bin / Ding, Wei. AutoEMage: automatic data transfer, preprocessing, real-time display and monitoring in cryo-EM. 2023. J. Applied Crystallography, Vol. 56, No. 6, p. 1865-1873 <br /> <br /> == Abstract ==<br /> <br /> Cryo-electron microscopy (cryo-EM), especially single-particle analysis, has<br /> become a powerful technique for visualizing the structure of biological<br /> macromolecules at high resolution. However, data acquisition in cryo-EM is<br /> time consuming because it requires the collection of thousands of images to<br /> achieve a high-quality reconstruction. Real-time preprocessing and display of<br /> the images can greatly enhance the efficiency and quality of data collection. This<br /> study presents AutoEMage, a new open-source software package that automates<br /> data transfer, preprocessing and real-time display in cryo-EM experiments.<br /> AutoEMage also includes a real-time data monitoring system that alerts users to<br /> issues with their data, allowing them to take corrective actions accordingly. The<br /> software is equipped with an easy-to-use graphical user interface that provides<br /> seamless data screening and real-time feedback on data quality and microscope<br /> status.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://www.nature.com/articles/s41592-023-02099-0<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

WikiSysop