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Insight II 的Profile

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发表于 2009-1-7 22:37:00 | 显示全部楼层 |阅读模式
据说Insight II 中有Profile-3D模块可以衡量模建结构的合理性,其中是不是有Score S的打分函数,其含义是什么?其在什么范围内说明模建结构合理?谢谢!
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发表于 2009-1-8 09:50:00 | 显示全部楼层
用过DS中的profile-3D,应该是一样的吧。
The Verify Protein (Profiles-3D) protocol allows you to evaluate the fitness of a protein sequence in its current 3D environment. It can be applied to assess the quality of a theoretical model or to examine the characteristics of an experimental structure. For example, it can be used to find hydrophobic patches on the surface of a structure.
To analyze the Verify score of the protein
The Verify score of the protein is the sum of the scores of all residues in the protein. This is a useful measure of the overall quality of the structure.
The Verify score is shown in the Molecule tab of the Data Table along with the expected high and low Verify scores for proteins of similar size. The expected high scores are based on a statistical analysis of high-resolution structures in the Protein Data Bank. The expected low score is 45 percent of the high score and is typical of grossly misfolded structures having this sequence length.
If the model structure has a Verify score higher than the expected high score, the structure is likely to be correct. If the overall quality score lies between the reference values, then some or all of the structure may be incorrect, and it deserves closer scrutiny. If the overall quality is lower than the expected low score, then the structure is almost certainly misfolded.
To analyze the Verify score of the amino acid residue
The Verify score of an amino acid residue indicates whether a residue is in the desired 3D environment. For example, a low score is given to a hydrophobic residue on a protein's surface and a polar residue in the protein's core. Regions of the protein over which the score approaches zero or becomes negative are likely to be misfolded. In homology modeling, a model region with a low score should be carefully examined and the model quality might be improved by adjusting low-scoring sequence alignments and rebuilding the model. On the other hand, if a surface patch of a protein shows a low Verify score, it may indicate that this surface is interacting with other proteins and should be buried internally.
To create a Line Plot of the residue score
  • In the Data Table, click the AminoAcid tab and select the Verify score column.
  • Choose the Line Plot command from the Chart menu to create a plot of the Verify score against the residue index. If there is more than one protein in the view, the Verify score for each molecule is shown in a separate line plot.
  • Selections on the line plot are reflected in the 3D Window. Hover the mouse over points on the line plot to see the residue ID and the Verify score value. When the Smooth Window Size parameter is larger than zero, the curve is smoothed using a running window averaging technique. Smoothing the curve in this way tends to average out spurious noise. The Window Size parameter specifies the size of the window (number of residues) used for the smoothing process. Smaller values produce higher resolution (but possibly noisier) curves. Window sizes in the range of 5-25 usually produce good results.
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     楼主| 发表于 2009-1-8 17:17:00 | 显示全部楼层
    非常感谢!!
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    发表于 2013-9-5 17:34:00 | 显示全部楼层
    本帖最后由 zhtear99 于 2013-9-5 17:37 编辑
    用过DS中的profile-3D,应该是一样的吧。
    The Verify Protein (Profiles-3D) protocol allows you to evaluate the fitness of a protein sequence in its current 3D environment. It can be applied to assess th ...
    guoyingying 发表于 2009-1-8 09:50
    你好,我用DS做同源建模,得到的模型DOPE score为-16,774.4,用Remachandran plot评价模型的时候,除了有一个氨基酸的点落在紫色区域(允许区)外,其他氨基酸的点都在蓝色区域(最适区)。接着用Profile-3D去评估模型,verify score=60.16, verify expected high score=66.5102,我看资料上讲verify score大于且接近verify expected high score的时候,模型是比较好的。我想请教下你,我做出的这个模型可靠不?可否用于后面做对接呢?
    另外,还想请教你两个问题。
    1. Profile-3D对应氨基酸的verify score分值在什么范围内是比较合适的?
    2.Profile-3D对应的某些氨基酸的verify score如果打分很低,如低于0.2,如何去优化呢?
    非常感谢您的解答~~~
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    发表于 2013-9-5 17:56:08 | 显示全部楼层
    编辑了很多次,还是这样,抱歉了,希望大家帮忙指点一下,多谢啦~
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