Analysis of the protein O00476.
- Secondary structure prediction (Jpred, PSIPRED, CONCORD)
- Detection of transmembrane segments (TOPCONS, Phobius)
- Homolog proteins search for template structures (PSI-BLAST, PSI-SEARCH)
- Finding of inward-open & outward-open templates
- Single-Template homology modelling (Swiss-model, Memoir for transmembrane protein)
- Multiple-Templates homology modelling (MODELER)
- Embedding model in a membrane (PPM server, iMembrane)
- Model refinement, especially loops and side-chains refinement (ModRefiner, SuperLooper, FalcLoop, Galaxy Refine, Scwrl4, SidePro, Rasp)
- Evaluation of the model (ProQ, Procheck)
- Normal modes analysis (NOMAD, WebNMA)
- MD coarse grain (OpenMM, Gromacs, with Martini force field)
- Docking (AutoDock ?)