Towards structural biology in the genus Mytilus: on-line homology modeling with Geno3D.
Seven structures from the genus Mytilus exist in the protein data bank (PDB) but > 1000 Mytilus protein sequences are known. Sequences (NCBI) were used as targets for on-line homology modeling with Geno3D as an alternative route to structure. Quality comparators include root mean square deviation (RMSD) of target from template, chain geometry and Ramachandran diagram analysis. We modeled 17 Mytilus structures for mainly stress-response proteins relevant to biomonitoring. These model files are available as a first step towards a structural resource for Mytilus. Analysis suggests that they are structurally plausible with low RMSDs relative to targets. Ramachandran analysis suggests a small percentage of disallowed dihedral angles (in the range 0-6.86% for 15 of 17 models).
Sheehan
D
D
Proteomics Research Group, Department of Biochemistry, University College Cork, Ireland. d.sheehan@ucc.ie
O'Donovan
E
E
D000818:Animals; D002374:Catalase / Q000737:chemistry; D003198:Computer Simulation; D030562:Databases, Protein; D004784:Environmental Monitoring; D006360:Heat-Shock Proteins / Q000737:chemistry*; D006801:Humans; D008956:Models, Chemical; D049878:Mytilus / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry
D006360:Heat-Shock Proteins; D011506:Proteins; D002374:Catalase