title: FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
abstract: CONCLUSIONS
  The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. However, the existing threading tools perform poorly on remote homologous proteins. Thus, improving fold recognition for remote homologous proteins remains a challenge. Besides, the proteome-wide structure prediction poses another challenge of increasing prediction throughput. In this study, we presented FALCON@home as a protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly variable regions. The highly variable regions lead to vague alignments in threading approaches. Thus, FALCON@home first extracts conserved regions from each template and then aligns a query protein with conserved regions only rather than the full-length template directly. This helps avoid the vague alignments rooted in highly variable regions, improving remote homologue identification. We implemented FALCON@home using the Berkeley Open Infrastructure of Network Computing (BOINC) volunteer computing protocol. With computation power donated from over 20,000 volunteer CPUs, FALCON@home shows a throughput as high as processing of over 1000 proteins per day. In the Critical Assessment of protein Structure Prediction (CASP11), the FALCON@home-based prediction was ranked the 12th in the template-based modeling category. As an application, the structures of 880 mouse mitochondria proteins were predicted, which revealed the significant correlation between protein half-lives and protein structural factors.
  
  
  METHODS
  FALCON@home is freely available at http://protein.ict.ac.cn/FALCON/.
  
  
  BACKGROUND
  shuaicli@cityu.edu.hk, dbu@ict.ac.cn
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Haicang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Wei-Mou
authors.initials: WM
authors.lastname: Zheng
authors.affiliation: Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, MO 65211, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Wang
authors.affiliation: College of Life Science, Huazhong University of Science and Technology, Wuhan, China and.
authors.forename: Kang
authors.initials: K
authors.lastname: Ning
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Shiwei
authors.initials: S
authors.lastname: Sun
authors.affiliation: Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.
authors.forename: Shuai Cheng
authors.initials: SC
authors.lastname: Li
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D057166:High-Throughput Screening Assays; D051379:Mice; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins