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首页> 外文期刊>Journal of Molecular Biology >Extending the accuracy limits of prediction for side-chain conformations.
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Extending the accuracy limits of prediction for side-chain conformations.

机译：扩展了侧链构象预测的准确性限制。

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摘要

Current techniques for the prediction of side-chain conformations on a fixed backbone have an accuracy limit of about 1.0-1.5 A rmsd for core residues. We have carried out a detailed and systematic analysis of the factors that influence the prediction of side-chain conformation and, on this basis, have succeeded in extending the limits of side-chain prediction for core residues to about 0.7 A rmsd from native, and 94 % and 89 % of chi(1) and chi(1+2 ) dihedral angles correctly predicted to within 20 degrees of native, respectively. These results are obtained using a force-field that accounts for only van der Waals interactions and torsional potentials. Prediction accuracy is strongly dependent on the rotamer library used. That is, a complete and detailed rotamer library is essential. The greatest accuracy was obtained with an extensive rotamer library, containing over 7560 members, in which bond lengths and bond angles were taken from the database rather than simply assuming idealized values. Perhaps the most surprising finding is that the combinatorial problem normally associated with the prediction of the side-chain conformation does not appear to be important. This conclusion is based on the fact that the prediction of the conformation of a single side-chain with all others fixed in their native conformations is only slightly more accurate than the simultaneous prediction of all side-chain dihedral angles. Copyright 2001 Academic Press.
机译：用于预测固定主链上侧链构象的当前技术对核心残基的准确度限制为约1.0-1.5 A rmsd。我们已对影响侧链构象预测的因素进行了详细而系统的分析，并在此基础上成功地将核心残基的侧链预测范围从天然的扩展到了约0.7 A rmsd。分别正确地预测到chi（1）和chi（1 + 2）二面角的94％和89％在自然角20度以内。这些结果是使用仅考虑范德华相互作用和扭转势的力场获得的。预测准确性在很大程度上取决于所使用的旋转异构体库。也就是说，一个完整而详细的rotamer库是必不可少的。使用包含超过7560个成员的广泛的旋转异构体库可以获得最高的准确度，其中从数据库中获取键长和键角，而不是简单地假设理想值。也许最令人惊讶的发现是，通常与侧链构象的预测相关的组合问题似乎并不重要。该结论基于以下事实：对单个侧链构象的预测与所有其他固定在其天然构象中的预测相比，对所有侧链二面角的同时预测仅稍精确一些。版权所有2001学术出版社。

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