Document Type

Article

Publication Date

2013

DOI

10.5936/csbj.201302003

Publication Title

Computational and Structural Biotechnology Journal

Volume

5

Issue

6

Pages

e201302003 (10pg.)

Abstract

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

Comments

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly cited.

Original Publication Citation

Li, Y. (2013). Conformational Sampling In Template-Free Protein Loop Structure Modeling: An Overview. Computational and Structural Biotechnology Journal, 5(6) e201302003. doi: 10.5936/csbj.201302003

ORCID

0000-0003-0178-1876 (Yaohang Li)

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