Skip to main content
padlock icon - secure page this page is secure

Glocal: Reconstructing Protein 3D Structure from 2D Contact Map by Combining Global and Local Optimization Schemes

Buy Article:

$63.00 + tax (Refund Policy)

Prediction of protein 3D structure from solely its amino acid sequence is one of the most challenging problems in structural bioinformatics, where the 3D structure reconstruction from observed constraints is the key step. In this paper, we propose a novel protocol called Glocal to recover a protein’s 3D coordinates based on a given 2D contact map by combining both global and local optimization schemes achieved by the swarm intelligence of Particle Swarm Optimization (PSO) and the Simulated Annealing (SA) techniques respectively. Our results demonstrate that Glocal can recover the 3D structures with the average RMSD less than 2 Å from the native contact map. Further analysis also shows that Glocal is powerful for handling with noisy contact map with the proposed combination optimization approaches.
No References
No Citations
No Supplementary Data
No Article Media
No Metrics

Keywords: Glocal; Simulated Annealing; Threshold; particle swarm optimization; protein; protein contact map; protein structure reconstruction; resolutions; simulated annealing

Document Type: Research Article

Affiliations: Department of Automation, Shanghai Jiao Tong University, Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.

Publication date: 01 June 2012

More about this publication?
  • Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a wide range of the integration of biology with computer and information science.

    The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.

    Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.
  • Access Key
  • Free content
  • Partial Free content
  • New content
  • Open access content
  • Partial Open access content
  • Subscribed content
  • Partial Subscribed content
  • Free trial content
Cookie Policy
Cookie Policy
Ingenta Connect website makes use of cookies so as to keep track of data that you have filled in. I am Happy with this Find out more