Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.
Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.
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DOI：
10.1002/prot.24341
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发表时间：
2014-02
影响因子：
2.9
通讯作者：
Zhang, Yang
中科院分区：
文献类型：
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作者：
Zhang, Yang
我们在CASP10中开发并测试了一种新的流程，用于基于I - TASSER和QUARK的相互作用来预测蛋白质结构，针对自由建模（FM）和基于模板的建模（TBM）目标。最值得注意的观察结果是，使用基于QUARK的从头算模型作为探针对穿线模板库进行筛选，可以检测到远距离同源模板，而这些模板可能会被传统的基于序列谱的穿线比对算法所忽略。通过I - TASSER进一步对模板组装进行优化，成功折叠了两个具有>150个残基的中等大小的FM目标。对于TBM，来自LOMETS的多重穿线比对首次被纳入从头算的QUARK模拟中，然后通过I - TASSER组装优化进一步完善。与传统的穿线组装优化程序相比，包含穿线约束的从头算折叠模型能够持续提高全长模型的质量，这通过GDT - HA和氢键得分来评估。尽管取得了成功，但在域边界预测以及非同源目标的中等大小蛋白质（特别是β - 蛋白质）的一致折叠方面仍然存在重大挑战。开发灵敏的折叠识别和从头算折叠方法对于解决这些问题至关重要。
We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems.
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通讯作者：
Zhang, Yang
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