Abstract
BackgroundContact 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.ResultsWe use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional 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 with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the Cβ atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity.ConclusionsThus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap.
Highlights
Contact maps have been extensively used as a simplified representation of protein structures
We used our reconstruction software to recreate the 3D structures based solely in the information supplied by the contact maps
To measure the accuracy we proceed by evaluating the RMSD of the generated models with the original structure
Summary
Contact maps have been extensively used as a simplified representation of protein structures. For over 30 years [1,2] contact maps have been used as an alternative representation of protein structures. A contact map is a 2-dimensional representation of the residue interactions in a protein structure. This 2-dimensional representation takes the form of a binary matrix. One can see this description from another perspective as a residue interaction graph (RIG) with residues as nodes and the contacts as edges.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have