Christian's Bookmarks

Sequence and structure analysis

Sequence analysis
- BLAST @ NCBI
  Compare your sequence against the NCBI databases
- EMBL-EBI Job Dispatcher
  Access all sequence analysis tool at the European Bioinformatics Institute (alignment, similarity search, translation, phylogeny etc.)
- Phylogeny.fr
  Robust Phylogenetic Analysis For The Non-Specialist
- ProtParam
  Computation of various sequence-based parameters of proteins (MW, pI, extinction coefficient etc.)
- SignalP 6.0
  Prediction of signal peptides
Structure analysis
- Getarea
  Calculate the solvent-accessible surface area of a protein
- Curie Bioinformatics server
  Services for analyzing protein structures and allergens
- CASTpFold
  Calculate cavities and voids in protein structures
- Aggrescan4D
  Structure-based prediction of the aggregation propensity of a protein
- CABS-flex 3.0
  Simulation of the stuctural flxibility of proteins and peptides
Protein structure modelling
- SwissModel
  Homology modelling at the Expasy server
- ProteinIQ
  Plattform to run AI-based protein modelling and design tools
- AlphaFold Server
  AI-powered prediction of the strucutures of biological macromolecules
- ESMfold
  Fast single-sequence protein structure prediction with multimer support
- RosettaFold3
  Open-source structure prediction for proteins, nucleic acids, and ligands