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期刊缩写|文章题目
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<strong data-brushtype="text" style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">食安园地 </strong>
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<strong data-brushtype="text" style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;"> 文献解读</strong>
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<span data-brushtype="text" style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">202X X X 星期X</span>
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<strong style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">NO.XX</strong>
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期刊题目
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<strong style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">导读</strong>
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<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; text-indent: 2em; caret-color: red; font-size: 14px; line-height: 1.5em; visibility: visible;font-family:微软雅黑, "Microsoft YaHei";">例：大家好，今天与大家分享一篇发表在</span><span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; text-indent: 2em; caret-color: red; color: #548dd4; font-size: 14px; line-height: 1.5em; visibility: visible;"><strong style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;"><span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;font-family:微软雅黑, "Microsoft YaHei";"><em style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; font-style: italic; visibility: visible;">Science</em></span></strong></span><span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; text-indent: 2em; caret-color: red; font-size: 14px; line-height: 1.5em; visibility: visible;font-family:微软雅黑, "Microsoft YaHei";">上的文章，文章的题目是“<strong style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;"><span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; text-indent: 2em; caret-color: red; line-height: 1.5em; color: #548dd4; visibility: visible;">Enzyme function prediction using contrastive learning</span></strong>”。</span><span style="font-size: 14px; color: var(--weui-FG-HALF); caret-color: red;font-family:微软雅黑, "Microsoft YaHei";">该研究提出并开发了基于对比学习的CLEAN模型，用于酶功能预测，通过在两个独立数据集上的验证，CLEAN模型表现出显著优于现有工具的准确性和可靠性，特别是在注释未研究酶、纠正错误标记和识别多功能酶方面，并通过实验验证了其在实际应用中的有效性。</span>
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<strong style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">0</strong><strong data-num="2" style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">1</strong>
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<strong style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">研究概括</strong>
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<p style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; clear: both; min-height: 1em; text-indent: 32px; line-height: 25.5px; visibility: visible;text-align:justify;" align="justify">
<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; font-size: 14px; line-height: 1.5em; visibility: visible;font-family:微软雅黑, "Microsoft YaHei";">随着DNA测序技术的发展，大量的新的蛋白质序列被发现，但其中绝大多数蛋白质的功能尚未明确，因此研究酶功能注释具有重要意义。现有的计算工具在预测这些功能尚未清楚的蛋白质时准确性不足，特别是对那些之前未被充分研究或具有多种活性的酶的注释效果较差，这严重制约了基因组学、合成生物学和生物催化等领域的进步。</span>
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<p style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; clear: both; min-height: 1em; text-indent: 32px; line-height: 25.5px; visibility: visible;text-align:justify;" align="justify">
<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; font-size: 14px; line-height: 1.5em; visibility: visible;font-family:微软雅黑, "Microsoft YaHei";">为了提供一种更准确、可靠和灵敏的酶功能注释方法，该研究提出并开发了CLEAN模型，用于解决现有工具的局限性。通过使用对比学习框架，CLEAN能够更好地处理序列相似性低、数据不平衡的问题，显著提升酶功能预测的准确性，从而推动生物医学和生物技术领域的发展。</span>
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<strong data-original-title="" title="" data-num="3" style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important;">02</strong>
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<p style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; clear: both; min-height: 1em; text-indent: 32px; line-height: 25.5px;">
<span style="color: #333333; text-align: justify; caret-color: #ff0000; text-decoration-thickness: initial; margin: 0px; padding: 0px; outline: 0px; max-width: 100%; font-size: 14px; line-height: 1.5em; box-sizing: border-box !important; overflow-wrap: break-word !important;font-family:微软雅黑, "Microsoft YaHei";">使用UniProt中的高质量数据，选取氨基酸序列作为输入，利用语言模型ESM-1b的表示作为输入的初始嵌入。</span><span style="font-size: 14px; color: var(--weui-FG-HALF); caret-color: red;font-family:微软雅黑, "Microsoft YaHei";">模型通过最小化正样本和锚点样本之间的欧几里得距离和最大化负样本和锚点样本之间的欧几里得距离进行训练。</span><span style="color: var(--weui-FG-HALF); caret-color: red; font-size: 14px;font-family:微软雅黑, "Microsoft YaHei";">根据这些距离来确定查询序列最可能的EC编号。距离越小，相似性越高，查询序列越可能具有该EC编号。</span>
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<span style="font-size: 14px;font-family:微软雅黑, "Microsoft YaHei";">当作为分类模型时，如上图C中所示，<span style="color: #333333; font-size: 14px; text-align: justify; text-indent: 32px; caret-color: #ff0000; text-decoration-thickness: initial; display: inline !important; ;font-family:微软雅黑, "Microsoft YaHei";">采用了最大分离和P值两种方法，分别按照距离大小和P值大小进行排序，</span>从排序顺序对EC数的可信预测进行优先排序。</span>
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<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; caret-color: red; font-size: 14px; line-height: 1.5em;font-family:微软雅黑, "Microsoft YaHei";">作者将CLEAN模型与其他最先进的EC编号预测工具进行不同方面的比较，图中展示了六个部分（A-F）。图A-C在不同的数据集中从准确率、召回率和F1评分三个方面将CLEAN模型与其他流行的EC预测工具进行比较。结果显示，只有ProteInfer模型在</span><span style="color: var(--weui-FG-HALF); caret-color: red; font-size: 14px;font-family:微软雅黑, "Microsoft YaHei";">代表性不足的EC编号数据集上的准确率比CLEAN模型高1.4%（图C），其他所有指标在三个数据集上CLEAN模型都具有优势，尤其是在NEW-392（图A）和Price-149（图B）数据集中，CLEAN模型的性能均大幅领先其他模型。</span>
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<span style="color: var(--weui-FG-HALF); caret-color: red; font-size: 14px;font-family:微软雅黑, "Microsoft YaHei";">图D展示了CLEAN模型在测试集中的准确率和召回率，基于EC编号在训练集中出现次数的不同分箱（binned）进行统计和比较，结果显示当EC编号在训练集中出现小于5次时，准确率和召回率相对较低，大于5次时，模型往往具有良好的性能。如图E所示，ProteInfer和DeepEC表现出对出现次数多的EC编号的偏向，而CLEAN模型始终保持较大优势。</span>
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<p style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; clear: both; min-height: 1em; text-indent: 32px; line-height: 25.5px;text-align:left;" align="left">
<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; caret-color: red; font-size: 14px; line-height: 1.5em;font-family:微软雅黑, "Microsoft YaHei";">上图展示了CLEAN模型在未注释的卤化酶（halogenases）上的实验验证，具体包括准确性热图、序列同一性热图、反应示意图、三维结构叠合、HPLC分析和质谱分析。图A显示了36种已识别的卤化酶的EC编号预测准确性，颜色越深代表准确率越高，CLEAN模型在几乎所有组别上都先显示出较高的准确性，明显优于其他模型。由图D可以看出，尽管SAM结合酶结构相似，但CLEAN仍能分辨他们。图E</span><span style="color: var(--weui-FG-HALF); text-align: justify; caret-color: red; font-size: 14px;font-family:微软雅黑, "Microsoft YaHei";">解释了不同酶催化下的具体化学反应，为功能预测提供生化证据，进一步通过HPLC分析（图F-K）和质谱分析（图L-Q）验证了CLEAN模型的预测。</span>
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<strong style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">0</strong><strong data-num="2" style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">3</strong>
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<strong style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; visibility: visible;">研究结论</strong>
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</section><span style="font-size: 14px;font-family:微软雅黑, "Microsoft YaHei";"> CLEAN模型通过对比学习显著提高了酶功能预测的准确性、可靠性和灵敏性，特别是在处理未研究和多功能酶方面表现出色，实验验证进一步证明了其在生物信息学和酶功能注释中的广泛应用潜力和有效性。</span>
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<p style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; clear: both; min-height: 1em; box-sizing: border-box !important; overflow-wrap: break-word !important;">
<span style="font-size: 9px; margin: 0px; padding: 0px; outline: 0px; max-width: 100%; color: black; letter-spacing: 1px; background: white; box-sizing: border-box !important; overflow-wrap: break-word !important;font-family:"Microsoft YaHei UI", sans-serif;">文献分享：</span><span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; color: black; letter-spacing: 1px; background: white; font-size: 12px; box-sizing: border-box !important; overflow-wrap: break-word !important;font-family:宋体, SimSun;">王修哲</span>
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<span style="font-size: 9px; margin: 0px; padding: 0px; outline: 0px; max-width: 100%; color: black; letter-spacing: 1px; background: white; box-sizing: border-box !important; overflow-wrap: break-word !important;font-family:"Microsoft YaHei UI", sans-serif;">文章链接：</span><span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; color: black; letter-spacing: 1px; background: white; box-sizing: border-box !important; overflow-wrap: break-word !important; font-size: 12px;"><span style="font-family:宋体, SimSun;">https://www.science.org/doi/full/10.1126/science.adf2465</span></span>
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<p style="font-size: var(--articleFontsize); margin: 0px; padding: 0px; outline: 0px; max-width: 100%; clear: both; min-height: 1em; box-sizing: border-box !important; overflow-wrap: break-word !important;">
<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; font-size: 9px; color: black; letter-spacing: 1px; background: white;font-family:"Microsoft YaHei UI", sans-serif;">文章引用：</span><span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; font-size: 12px; line-height: 1.58em; box-sizing: border-box !important; overflow-wrap: break-word !important;font-family:宋体, SimSun;">YU T, CUI H, LI J C, et al. Enzyme function prediction using contrastive learning [J]. Science, 2023, 379(6639): 1358-63.</span>
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<strong data-brushtype="text" style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important;">文献分享阅读</strong>
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<span data-brushtype="text" style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important;">微信号：食安园地</span>
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<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; font-size: 12px;">《食安园地》微信公众号所使用的文章和图片属于相关权利人所有。因客观原因，如存在不当使用的情况，敬请相关权利人随时与我们联系及时处理。</span><br style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important;"/>
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<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; font-size: 12px;">邮箱：mrzhang9704@163.com</span>
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<span style="margin: 0px; padding: 0px; outline: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; font-size: 12px;" > 电话/微信：15102978114</span>
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