以下内容来自殷赋科技微信学术交流群。
一
A:对接的时候,小分子与蛋白的活性位点是怎么选呢?参照文献么?选择的时候,活性位点有很多,是选择什么样的位点对接呢?
B:先分析你的化合物和已知底物的相似性关系,再选择合适位点。
A:我刚刚开始接触这些,不太懂,相似性关系是分析哪方面呢?
B:拓扑结构相似性,电荷分部的相似性。一类化合物能结合多个口袋的话,那结合就是竞争性的。挨个dock,最后把结果放在一起可以分析。也可以先看一下文献有没有特殊位点比如离子通道蛋白就有这种例子。主要看你的目标来定。
殷赋科技:看看我们公众号的文章,《如何确定对接口袋》。总的原则是,尽可能依靠来自实验或文献的信息来确定对接口袋,其次是软件预测。如果没有任何信息可以帮助你选择或确定唯一的对接口袋,那就全部都用,分别做对接,再分析对接结果。有条件的,再做实验验证,比如定点突变。
Mr.Nerve-中国药科大学:使用薛定谔时,如何对某一部分进行片段取代,取代成各种各样的基团,然后批量对接,这可以实现吗?
殷赋科技:MOE可以实现,不知道薛定谔能不能。
Mr.Nerve-中国药科大学:那我用MOE弄成sdf格式,然后批量对接对吗?取代片段可以自行选择吧,不一定要用内置库吧?
殷赋科技: 如果要用自己的片段库,需要处理成MOE能够使用的格式。请看MOE的说明。当然也可以先生成化合物库再对接,这就跟一般的对接流程没啥区别了。
二
A:知道纳米材料的官能团和一段氨基酸序列,可以推测两者能不能发生相互作用吗?
B:可以。
A:怎么推测?
B:生物材料?
A:不知道,老板就给了官能团和氨基酸序列。
B:我们组都是建模跑md,看结合能力。
A:那段序列找不到模板建模,也不知材料结构。
C:同源建模需要模板,序列足够长时才能用; 序列短,不能用该方法。因为序列太短,不能满足Do Littles提出的同源家族判断标准。太短,也没有一定的稳定构象,而是柔性不断变化。很短的,按有机小分子进行构象搜索就可以。
A:是不是必须要建模,采用对接方式,让两者发生作用?那段氨基酸序列有50个氨基酸。
C:50个氨基酸做不了同源建模预测3d结构。做实验都比计算快,可以用核磁或生物质谱。
A:那意思预测不了?
C:我是说同源建模没法做,可以试试其它的方法。比如,你有核磁知道两个原子间距离,用距离约束再进行计算就会比纯计算准确。
A:啥也没有,我连材料结构都不知道。
D:50个aa完全可以做de novo prediction。可以先做个二级结构预测,如果是coil居多,就不用提交robetta了。
三
A:各位老师,请问如何用MOE计算蛋白口袋氨基酸的序列一致性呢?
殷赋科技:在SEQ界面,找到alignment。
殷赋科技:选择口袋残基,看看是不是一样的,或者相似的,数值看alignment的similarity。
A:选择select就显示这样了。
B:点击similarity,Metric>similarity。
A:similarity也是一样呐。
B:是否同时选中了两条链呢?
A:如果我想看口袋附近氨基酸残基的一致性呢?
B:Moe 叠合pockets, 需要在『align/superpose』做出调整。里面有多种option。自己尝试下就好了。
更多资讯,请访问www.yinfotek.com或关注微信公众号“殷赋科技”。想加入微信学术交流群的朋友,请在公众号首页输入“加群”,验证后入群。
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