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<span class="blog-description">A nook to hoard my manuscripts.</span>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-03-25-summary-doi.org/10.48550/arXiv.2302.01129.html" rel="bookmark" title="Permalink to 文献总结｜通过连接感知模版挖掘实现从头生成分子">文献总结｜通过连接感知模版挖掘实现从头生成分子</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 3月25日">2023年 3月25日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
本文介绍由中科大于 2023 年发布在 ICLR 2023 上的一篇文章，文章原标题为 De Novo Molecular Generation via Connection-aware Motif Mining，文章提出了一种从分子数据集中挖掘模版结构的算法，同时设计了一种通过组合模版结构实现分子生成的模型。
</p>
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<aside class="post-tags">
<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/gnn.html"># GNN</a><a href="https://leonis.cc/tag/vae.html"># VAE</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/zai-lu-shang/2023-03-24-spring-trip-in-tianjin.html" rel="bookmark" title="Permalink to 春日漫步小记">春日漫步小记</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 3月24日">2023年 3月24日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/zai-lu-shang.html">在路上</a>
</span>
<p class="post-excerpt">
五六天前刚起了几阵沙尘暴，入眼的一切都是黄蒙蒙的。黄沙中的行人都拉紧着衣服、戴着口罩，可能是为了防沙，也可能是为了防病毒。唯一不避风沙的只有两旁的行道树，经冬之后满是枯枝，更添了几分萧索。就是在这样一片了无生气之中，竟在 …
</p>
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<aside class="post-tags">
<a href="https://leonis.cc/tag/sui-bi.html"># 随笔</a><a href="https://leonis.cc/tag/you-ji.html"># 游记</a><a href="https://leonis.cc/tag/she-ying.html"># 摄影</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-03-17-summary-doi.org/10.48550/arXiv.2210.13695.html" rel="bookmark" title="Permalink to 文献总结｜使用等变扩散模型进行基于结构的药物设计">文献总结｜使用等变扩散模型进行基于结构的药物设计</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 3月17日">2023年 3月17日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
本文介绍由洛桑联邦理工学院等研究单位于 2022 年发布在 arXiv 上的一篇文章，文章原标题为 Structure-based Drug Design with Equivariant Diffusion Models，文章首次将等变扩散模型用于基于结构的药物设计，实现针对特定的蛋白靶点生成多样且具有高亲合力的的配体分子。
</p>
<div class="post-excerpt">
<aside class="post-tags">
<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/gnn.html"># GNN</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-03-14-deploy-pelican-search.html" rel="bookmark" title="Permalink to 为 Pelican 博客加入搜索功能">为 Pelican 博客加入搜索功能</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 3月14日">2023年 3月14日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
博客上的文章越来越多了，靠文章 tag 来检索文章总是有些麻烦，不妨为博客配置一个搜索功能吧。在中文互联网上搜索不到半点配置 Pelican Search 的相关信息，希望这篇文章能帮到后来人。
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<a href="https://leonis.cc/tag/blog.html"># Blog</a><a href="https://leonis.cc/tag/pelican.html"># Pelican</a><a href="https://leonis.cc/tag/rust.html"># Rust</a><a href="https://leonis.cc/tag/windows.html"># Windows</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-03-11-summary-doi.org/10.48550/arXiv.2209.06158.html" rel="bookmark" title="Permalink to 文献总结｜为蛋白质口袋定制分子：用于基于结构药物设计的 Transformer 分子生成方法">文献总结｜为蛋白质口袋定制分子：用于基于结构药物设计的 Transformer 分子生成方法</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 3月11日">2023年 3月11日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
本文介绍由微软研究团队于 2022 年发布在 arXiv 上的一篇文章，文章原标题为 Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design，文章使用 Transformer 构建了一种能够获取受体 3 维信息的分子生成模型 TamGent，其中分子生成部分使用了预训练模型，避免了训练数据有限的问题。
</p>
<div class="post-excerpt">
<aside class="post-tags">
<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/transformer.html"># Transformer</a><a href="https://leonis.cc/tag/vae.html"># VAE</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-03-03-summary-doi.org/10.1021/acs.jcim.1c00600.html" rel="bookmark" title="Permalink to 文献总结｜MolGPT：使用 Transformer 解码器模型实现分子生成">文献总结｜MolGPT：使用 Transformer 解码器模型实现分子生成</a>
</h2>
<span class="post-meta">
<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 3月03日">2023年 3月03日</time>
| Archived in
<a class="post-meta-tag" href="https://leonis.cc/category/sui-sui-nian.html">碎碎念</a>
</span>
<p class="post-excerpt">
本文介绍于 2022 年发表在 Journal of Chemical Information and Modeling 上的一篇文章，文章原标题为 MolGPT: Molecular Generation Using a Transformer-Decoder Model，在 GPT 模型已经在自然语言处理领域得到了成功应用的背景下，这篇文章首次将 GPT 模型应用于完成分子生成的任务，实现了分子性质和结构两个方面的优化。
</p>
<div class="post-excerpt">
<aside class="post-tags">
<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/transformer.html"># Transformer</a><a href="https://leonis.cc/tag/gpt.html"># GPT</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-02-25-summary-doi.org/10.1021/ci900450m.html" rel="bookmark" title="Permalink to 文献总结｜在大数据集中有效识别匹配分子对（MMPs）的算法">文献总结｜在大数据集中有效识别匹配分子对（MMPs）的算法</a>
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<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 2月25日">2023年 2月25日</time>
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本文介绍于 2010 年发表在 Journal of Chemical Information and Modeling 上的一篇文章，文章原标题为 Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets，文章介绍了一种在大规模数据中识别匹配分子对的算法，这种算法也就是目前用于生成匹配分子对的最常用方法。
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<a href="https://leonis.cc/tag/literature-summary.html"># Literature Summary</a><a href="https://leonis.cc/tag/cadd.html"># CADD</a><a href="https://leonis.cc/tag/algorithm.html"># Algorithm</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-02-22-create-pelican-plugin.html" rel="bookmark" title="Permalink to 为 Pelican 博客写插件——在文章中插入豆瓣图书">为 Pelican 博客写插件——在文章中插入豆瓣图书</a>
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<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 2月22日">2023年 2月22日</time>
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突然想把豆瓣图书信息插入到文章中，便于在博客里记录阅读笔记。寻找了一圈无果，只好自己动手写个插件，也正好研究了下 Pelican 插件的工作方式。
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<a href="https://leonis.cc/tag/blog.html"># Blog</a><a href="https://leonis.cc/tag/pelican.html"># Pelican</a><a href="https://leonis.cc/tag/python.html"># Python</a><a href="https://leonis.cc/tag/xpath.html"># XPath</a> </aside>
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-02-17-summary-doi.org/10.1038/s42256-022-00580-7.html" rel="bookmark" title="Permalink to 文献总结｜通过大规模化学语言表示捕获分子结构和性质">文献总结｜通过大规模化学语言表示捕获分子结构和性质</a>
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<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 2月17日">2023年 2月17日</time>
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本文介绍于 2022 年发表在 Nature Machine Intelligence 上的一篇文章，文章原标题为 Large-scale chemical language representations capture molecular structure and properties，文章使用大量来自 PubChem 和 ZINC 的分子训练了基于 Transformer 的化学语言模型，该模型将原始的 SMILES...
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<h2 class="post-title"><a href="https://leonis.cc/sui-sui-nian/2023-02-13-deploy-pelican-by-nginx.html" rel="bookmark" title="Permalink to Pelican + Nginx 在服务器上搭载静态博客">Pelican + Nginx 在服务器上搭载静态博客</a>
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<a class="post-meta-tag" href="https://leonis.cc/author/leo.html">Leo</a>
| <time datetime="2023年 2月13日">2023年 2月13日</time>
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去年购置了一个服务器，由于后来太忙，一直没有时间折腾，终于有一段空闲的时间了，就尝试把我的 Pelican Blog 从 GitHub Pages 搬迁到服务器上，再通过 Nginx 部署我的站点。
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