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Databases

  • SwissSidechain  •  SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins.  [less]

Tools

  • SWISS-MODEL Workspace  •  SWISS-MODEL is a fully automated web based protein structure homology-modeling expert system. The SWISS-MODEL Workspace is a web-based integrated service which assist and guides the user in building protein homology models at different levels of complexity. A personal working environment (workspace), where several modelling projects can be carried out in parallel, is provided for each user. [less]
  • OpenStructure  •  The OpenStructure library project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested users and method developers in the field of structural bioinformatics. Its cleanly designed API available in both Python an C++ provides a command line interface for batch processing as well as a graphical user interface fully scriptable in Python. [less]
  • QMEAN  •  Estimating the quality of predicted structural models is a crucial step in homology modeling. Scoring functions analyze different structural features of the protein models in order to generate a quality estimate. QMEAN consists of four statistical potential terms (two non-bonded interaction terms, a torsion angle term and a solvation term) and two components describing the agreement between predicted and observed secondary structure and solvent accessibility. [less]
  • SwissParam  •  SwissParam is a fully automatic server that provides topology and parameters for small organic molecules, compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS. [less]