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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » Gromacs/Amber/NAMD » 【求助】紧急求助
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wgpig

木虫 (小有名气)
★ ★ ★ ★ ★
dolphin100(金币+1,VIP+0):感谢热心帮忙
lei0736(金币+4,VIP+0):谢谢
编辑掉了。

[ Last edited by wgpig on 2009-1-5 at 22:47 ]
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11楼2009-01-05 16:33:29
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dolphin100

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谢谢 热心帮忙!
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Constanteffortscanyieldsuresuccess!
12楼2009-01-06 00:21:32
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zz422

铜虫 (小有名气)
我也是做动力学的，但不明白为什么要做native contact number？做native contact number能反应什么现象？
项大家请教了，
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13楼2009-01-07 17:29:41
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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 ]
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14楼2009-01-07 19:17:44
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