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dolphin100

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修回稿中审稿人让计算蛋白质的native contact number?什么软件可以做啊
本人做了个MD实验,有轨迹文件, 用什么软件计算得到?如何计算? VMD,insightII??......
由于稿子需要快速回复, 着急等待高手赐教!
不胜感激!

[ Last edited by zdhlover on 2009-12-10 at 15:06 ]

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1楼 2008-11-27 20:52:24

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wuhanhgf2002

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dolphin100(金币+1,VIP+0):谢谢支持!

In protein folding, a native contact is a contact between the side chains of two amino acids that are not neighboring in the amino acid sequence (i.e., they are more than three residues apart in the primary sequence) but are spatially close in the protein's native state tertiary structure. The fraction of native contacts reproduced in a particular structure is often used as a reaction coordinate for measuring the deviation from the native state of structures produced during molecular dynamics simulations or in benchmarks of protein structure prediction methods.

The contact order is a measure of the locality of a protein's native contacts; that is, the sequence distance between amino acids that form contacts. Proteins with low contact order are thought to fold faster and some may be candidates for downhill folding.

Nonnative contacts might be defined in various slightly different probabilistic ways, but roughly speaking, nonnative contacts are when amino acid resides that are more than three apart in the primary sequence make a contact (come within some distance from each other) in the transition state with a higher probability than they do in the native state.

我猜楼主的文章一定是关于蛋白质折叠或结构预测方面的吧。

[ Last edited by wuhanhgf2002 on 2009-1-7 at 19:20 ]