PEM-fitter: A Coarse-Grained Method to Validate Protein Candidate Models

Journal of computational biology: A journal of computational molecular cell biology

KamalAl Nasr^1¹  ChristopherJones^1² 

[1]Department of Computer Science, Tennessee State University, Nashville, Tennessee^1

[2]Department of Mathematics, The University of Jordan, Amman, Jordan^2

关键词: cryo-electron microscopy;    iterative closest point;    protein evaluation;    protein modeling;    skeleton;   

DOI  :  10.1089/cmb.2017.0191

学科分类：生物科学（综合）

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

The volumetric images produced by Cryo-Electron Microscopy (cryo-EM) technique are used to model macromolecular assemblies and machines. De novo protein modeling uses these images to computationally model the structure of the molecules. Many candidate conformations are usually generated during the intermediate step. Conventionally, each of these candidates is evaluated by time-consuming approaches such as potential energy. We introduce an initial version of a geometrical screening method that uses the skeleton of the cryo-EM images to evaluate candidate structures. The aim of this method is to reduce the number of native-like candidate conformations and, therefore, reduce the time required for structural evaluation by energy calculations. A test of two datasets was performed. The first dataset contains 10 proteins and shows that our method can successfully detect the correct native structure for the given skeleton among a set of different protein structures. The second dataset contains 12 proteins and shows that our method can filter slightly modified decoy conformations of the same protein. The efficiency of the method is also reported.

【 授权许可】

Unknown