%0 Journal Article
%T Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure
%A Marco Vassura
%A Pietro Di Lena
%A Luciano Margara
%A Maria Mirto
%A Giovanni Aloisio
%A Piero Fariselli
%A Rita Casadio
%J BioData Mining
%D 2011
%I BioMed Central
%R 10.1186/1756-0381-4-1
%X In this paper, by adopting a GRID technology, our algorithm for 3D reconstruction FT-COMAR is benchmarked on a huge set of non redundant proteins (1716) taking random noise into consideration and this makes our computation the largest ever performed for the task at hand.We can observe the effects of introducing random noise on 3D reconstruction and derive some considerations useful for future implementations. The dimension of the protein set allows also statistical considerations after grouping per SCOP structural classes.All together our data indicate that the quality of 3D reconstruction is unaffected by deleting up to an average 75% of the real contacts while only few percentage of randomly generated contacts in place of non-contacts are sufficient to hamper 3D reconstruction.A major problem of the genomic era is how to link the protein sequence to the protein structural and functional space. When no template with high sequence homology to the target is found in the Protein Data Base (PDB), then building by homology cannot be safely applied. In these cases the protein structure can be predicted with ab initio methods whose scoring capability is poor when no conserved structural domain is recognized in the target. Structural features, including structural conserved domains, disulfide bonds, protein secondary structure, residue solvent accessibility and how residues contribute to local stability (contact residues), can to some extent help in constraining the protein 3D structure. Residues are defined to be in contact in the protein structure when they interact within a fixed distance (threshold) that is routinely set at a value ¡Ý 7 £¿. Residue contact prediction was exploited with different approaches, including statistical and probabilistic methods [1]. In a contact map representation of the protein 3D structure, all the short and long range interactions promoting protein stability emerge to different extent depending on the threshold value adopted to compute the 2
%U http://www.biodatamining.org/content/4/1/1