title: Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation.
abstract: BACKGROUND
  Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy.
  
  
  RESULTS
  We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling.
  
  
  BACKGROUND
  CIS-RR is available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html.
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Cao
authors.forename: Lin
authors.initials: L
authors.lastname: Song
authors.forename: Zhichao
authors.initials: Z
authors.lastname: Miao
authors.forename: Yun
authors.initials: Y
authors.lastname: Hu
authors.forename: Liqing
authors.initials: L
authors.lastname: Tian
authors.forename: Taijiao
authors.initials: T
authors.lastname: Jiang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins