Towards structural biology in the genus Mytilus: On-line homology modeling with Geno3D

D. Sheehan, E. O'Donovan

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

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).

Original languageBritish English
Pages (from-to)S411-S414
JournalMarine Environmental Research
Volume62
Issue numberSUPPL. 1
DOIs
StatePublished - 2006

Keywords

  • Biomarker
  • Homology modeling
  • Mytilus
  • Protein
  • Stress-response
  • Structure

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