The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

We have developed the SWISSMODEL workspace to address this aspect by providing a range of tools that allow the user to validate and to modify the different modelling steps manually

Konstantin Arnold

2005

Scholarcy highlights

  • Three-dimensional protein structures are of great interest for the rational design of many different types of biological experiments, such as site-directed mutagenesis or structure-based discovery of specific inhibitors
  • For commercial re-use, please contact journals.permissions@oxfordjournals.org disordered regions can be predicted for the target sequence, suitable template structures identified by searching the SWISS-MODEL Template Library, and target–template alignments can be manually adjusted
  • We describe how the different modelling modes and tools available from the SWISS-MODEL workspace were applied to identify suitable templates and to build homology models for two biologically relevant human proteins: Cyclin A1 and Transmembrane Protease 3
  • Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles and in regulating cyclin-dependent kinases
  • Inactive CDK apoenzymes are partially activated by complex formation with regulatory cyclin subunits and the complexes are further activated by phosphorylation of a Thr residue in CDKs
  • While Cyclin A2 is widely expressed in different tissues, Cyclin A1 is limited to male germ cells
  • For the low-density lipoprotein receptor A domain only Iterative Profile Blast and HMM-based template identification methods are sensitive enough to detect potential structural templates with significant scores

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