Optimal contact definition for reconstruction of Contact Maps

Background: Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. Results: We use an implementation of the well-known distance geometry protocol to build realistic protein 3dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Jose M. Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis, Michael Lappe
• Keywords: BMCBI 2010, Contact Maps, Protein Structure, Structure Prediction