title: Computational Protein Design Under a Given Backbone Structure with the ABACUS Statistical Energy Function.
abstract: An important objective of computational protein design is to identify amino acid sequences that stably fold into a given backbone structure. A general approach to this problem is to minimize an energy function in the sequence space. We have previously reported a method to derive statistical energies for fixed-backbone protein design and showed that it led to de novo proteins that fold as expected. Here, we present the usage of the program that implements this method, which we now name as ABACUS (A Backbone-based Amino aCid Usage Survey).
authors.affiliation: School of Life Sciences, Hefei National Laboratory for Physical Sciences at the Microscales, and Collaborative Innovation Center of Chemistry for Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xiong
authors.affiliation: School of Life Sciences, Hefei National Laboratory for Physical Sciences at the Microscales, and Collaborative Innovation Center of Chemistry for Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China. chenquan@ustc.edu.cn.
authors.forename: Quan
authors.initials: Q
authors.lastname: Chen
authors.affiliation: School of Life Sciences, Hefei National Laboratory for Physical Sciences at the Microscales, and Collaborative Innovation Center of Chemistry for Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China. hyliu@ustc.edu.cn.|Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China. hyliu@ustc.edu.cn.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008958:Models, Molecular; D015233:Models, Statistical; D009154:Mutation; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D012984:Software; D064878:Web Browser
chemical_list: D011506:Proteins
keywords: Backbone structure; Mutation analysis; Protein design; Statistical energy function