Vajda Sandor, Camacho Carlos J
Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
Trends Biotechnol. 2004 Mar;22(3):110-6. doi: 10.1016/j.tibtech.2004.01.006.
Are current docking methods capable of building complexes from putative component protein structures? Results of recent computational studies, including those of the CAPRI (Critical Assessment of Protein Interactions) competition, were used to determine the key properties for successful docking and introduce a classification of protein complexes based on docking difficulty. Enzyme-inhibitor complexes could be determined with reasonable accuracy - possibly to within a few alternative structures. Results for antigen-antibody pairs are less predictable, and data for small signaling complexes are generally poor. However, moderate amounts of experimental data can remove uncertainty and the methodology is rapidly improving. Transient complexes with large interface areas undergo substantial conformational change and are beyond the reach of current docking methods. The docking of such complexes might therefore require fundamentally new approaches.
当前的对接方法能否根据假定的组成蛋白质结构构建复合物？包括蛋白质相互作用关键评估（CAPRI）竞赛在内的近期计算研究结果，被用于确定成功对接的关键特性，并引入基于对接难度的蛋白质复合物分类。酶-抑制剂复合物能够以合理的准确度确定——可能在几种替代结构范围内。抗原-抗体对的结果较难预测，而小信号复合物的数据通常较差。然而，适量的实验数据可以消除不确定性，并且该方法正在迅速改进。具有大界面区域的瞬时复合物会经历显著的构象变化，超出了当前对接方法的能力范围。因此，此类复合物的对接可能需要全新的方法。
