Three dimensional shape comparison of flexible proteins using the local-diameter descriptor.
Three dimensional shape comparison of flexible proteins using the local-diameter descriptor.
复制标题
DOI：
10.1186/1472-6807-9-29
复制
发表时间：
2009-05-12
影响因子：
--
通讯作者：
Ramani K
中科院分区：
文献类型：
--
作者：
Fang Y;Liu YS;Ramani K
通过比较它们的形状相似性来推断蛋白质功能的技术一直受到人们的极大关注。蛋白质是功能单位，其形状柔性在各种生物过程中起着至关重要的作用。一些形状描述符通过将蛋白质作为刚体来处理，从而证明了蛋白质形状比较的能力。但这可能会导致对柔性蛋白质形状的错误比较。我们介绍了一种通过采用局部直径(LD)描述符来比较柔性蛋白质形状的有效方法。最近开发的用于处理基于骨架的形状变形的LD描述符在本工作中被用于捕捉蛋白质骨架运动引起的形状变形的不变性。蛋白质表面上的每个采样点都被分配了一个值，测量该点附近的3D形状的直径。根据直径值的分布以一维直方图的形式构建LD描述符。基于直方图的形状表示将柔性蛋白质的形状比较问题简化为一维特征向量之间的简单距离计算。实验结果表明，该描述符能准确地处理蛋白质形状变形。此外，我们将LD描述子用于蛋白质形状检索，并将其与传统形状描述子的有效性进行了比较。敏感度-特异度图显示，在蛋白质家族的一致性和不同蛋白质家族的区分性方面，LD描述符比传统的形状描述符表现得更好。我们的研究为比较柔性蛋白质的形状提供了一种有效的技术。实验结果表明，LD描述子对蛋白质形状变形不敏感。该方法对于形状相似的分子检索和蛋白质结构的快速检索具有潜在的应用价值。上提供了演示和补充材料。
Techniques for inferring the functions of the protein by comparing their shape similarity have been receiving a lot of attention. Proteins are functional units and their shape flexibility occupies an essential role in various biological processes. Several shape descriptors have demonstrated the capability of protein shape comparison by treating them as rigid bodies. But this may give rise to an incorrect comparison of flexible protein shapes. We introduce an efficient approach for comparing flexible protein shapes by adapting a local diameter (LD) descriptor. The LD descriptor, developed recently to handle skeleton based shape deformations, is adapted in this work to capture the invariant properties of shape deformations caused by the motion of the protein backbone. Every sampled point on the protein surface is assigned a value measuring the diameter of the 3D shape in the neighborhood of that point. The LD descriptor is built in the form of a one dimensional histogram from the distribution of the diameter values. The histogram based shape representation reduces the shape comparison problem of the flexible protein to a simple distance calculation between 1D feature vectors. Experimental results indicate how the LD descriptor accurately treats the protein shape deformation. In addition, we use the LD descriptor for protein shape retrieval and compare it to the effectiveness of conventional shape descriptors. A sensitivity-specificity plot shows that the LD descriptor performs much better than the conventional shape descriptors in terms of consistency over a family of proteins and discernibility across families of different proteins. Our study provides an effective technique for comparing the shape of flexible proteins. The experimental results demonstrate the insensitivity of the LD descriptor to protein shape deformation. The proposed method will be potentially useful for molecule retrieval with similar shapes and rapid structure retrieval for proteins. The demos and supplemental materials are available on .
登录
查看更多内容
影响因子：
56.9
作者：
CONNOLLY, ML
通讯作者：
CONNOLLY, ML
影响因子：
0.6
作者：
Choi, HI;Choi, SW;Moon, HP
通讯作者：
Moon, HP
DOI：
10.1109/tcbb.2006.43
发表时间：
2006-07-01
影响因子：
4.5
作者：
Daras, Petros;Zarpalas, Dimitrios;Strintzis, Michael Gerassimos
通讯作者：
Strintzis, Michael Gerassimos
影响因子：
14.9
作者：
Holm, L;Sander, C
通讯作者：
Sander, C
DOI：
10.1098/rspa.2007.1823
发表时间：
2007-05-08
影响因子：
3.5
作者：
Ballester, Pedro J.;Richards, W. Graham
通讯作者：
Richards, W. Graham