Osguthorpe D J
School of Chemistry, University of Bath, United Kingdom.
Proteins. 1999;Suppl 3:186-93. doi: 10.1002/(sici)1097-0134(1999)37:3+<186::aid-prot23>3.3.co;2-4.
Structure predictions for nine targets from the CASP3 meeting are presented and compared with the experimental structure. These predictions are made using the simplified flexible geometry representation of protein structure and potentials which mimic the physical forces involved in protein folding with no help from multiple sequences. The major differences from the CASP2 potentials are identified, and the prediction successes and failures are related to the underlying potentials. Target T0065 was successfully folded from an extended chain to 3.8 A CA RMS of the native structure. The quality of the secondary structure component of all predictions was significantly improved, averaging a Q3 of 64%, which was spread evenly across the fold types, all alpha, alpha/beta mixed, and mainly beta. A number of the other predictions had a spatial arrangement of the secondary structure segments close to native, although the major problem with most predictions was the over-extension of secondary structure segments which often coalesced independent segments together. For target T0056 the ab initio prediction was the closest to the native structure of all methods including threading according to the Hubbard RMS coverage plots.
展示了来自第三届蛋白质结构预测技术关键评估（CASP3）会议的九个目标的结构预测，并与实验结构进行了比较。这些预测是使用蛋白质结构的简化灵活几何表示和势能进行的，这些势能模拟了蛋白质折叠过程中涉及的物理力，且没有多序列的帮助。确定了与第二届蛋白质结构预测技术关键评估（CASP2）势能的主要差异，并将预测的成功与失败与潜在的势能相关联。目标T0065从伸展链成功折叠至天然结构的3.8埃Cα均方根偏差（CA RMS）。所有预测的二级结构成分质量均有显著提高，平均Q3为64%，且在所有折叠类型（全α、α/β混合和主要为β）中均匀分布。其他一些预测的二级结构片段的空间排列接近天然结构，尽管大多数预测的主要问题是二级结构片段过度延伸，这些片段常常将独立的片段合并在一起。对于目标T0056，根据哈伯德均方根覆盖图，从头预测是所有方法（包括穿线法）中最接近天然结构的。
