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首页> 外文期刊>Journal of Molecular Biology >ICOSA: A Distance-Dependent, Orientation-Specific Coarse-Grained Contact Potential for Protein Structure Modeling
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ICOSA: A Distance-Dependent, Orientation-Specific Coarse-Grained Contact Potential for Protein Structure Modeling

机译：ICOSA：用于蛋白质结构建模的距离相关，方向特定的粗粒接触电位

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摘要

The relative distance and orientation in contacting residue pairs plays a significant role in protein folding and stabilization. We hereby devise a new knowledge-based, coarse-grained contact potential, so-called ICOSA, by correlating inter-residue contact distance and orientation in evaluating pair-wise inter-residue interactions. The rationale of our approach is to establish icosahedral local coordinates to estimate the statistical residue contact distributions in all spherical triangular shells within a sphere. We extend the theory of finite ideal gas reference state to icosahedral local coordinates. ICOSA incorporates long-range contact interactions, which is critical to ICOSA sensitivity and is justified in statistical rigor. With only backbone atoms information, ICOSA is at least comparable to all-atom, fine-grained potentials such as Rosetta, DFIRE, I-TASSER, and OPUS in discriminating near-natives from misfold protein conformations in the Rosetta and I-TASSER protein decoy sets. ICOSA also outperforms a set of widely used coarse-grained potentials and is comparable to all-atom, fine-grained potentials in identifying CASP10 models. (C) 2015 Elsevier Ltd. All rights reserved.
机译：接触残基对的相对距离和方向在蛋白质折叠和稳定中起重要作用。在此，我们通过评估残基间残基间相互作用之间的残基间接触距离和方向，设计了一种新的基于知识的粗粒度接触电势，即所谓的ICOSA。我们方法的基本原理是建立二十面体局部坐标，以估计球体内所有球形三角壳中的统计残差接触分布。我们将有限理想气体参考状态的理论扩展到二十面体局部坐标。 ICOSA结合了远程接触相互作用，这对于ICOSA的敏感性至关重要，并且在统计上也很严格。仅凭主链原子信息，ICOSA至少可与全原子，细粒度的电势（如Rosetta，DFIRE，I-TASSER和OPUS）相提并论，以区分Roses和I-TASSER蛋白质诱饵中错误折叠的蛋白质构象中的近天然套。在识别CASP10模型时，ICOSA还优于一组广泛使用的粗粒度电势，并且可与全原子，细粒度电势相比。 （C）2015 Elsevier Ltd.保留所有权利。

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