Grundlegende analytische Software Tools und Datenbanken
- Origin: Data analysis and graphing software: Support, Tutorials and Videos.
- National Centre for Biotechnology Information: Gene and protein Sequence databases, literature database
e.g. BLAST (Basic Local Alignment Search Tool)
- Worldwide protein data bank: Database of Macromolecule structures with further information on methods, workshops, online tools etc.
- The Cambridge Crystallographic Data Centre: Wordwide Data Bank for low molecular weight compounds.
- ExPASy: SIB Bioinformatics resource portal: Online tools for genetics, proteomics biophysics, imaging and modelling
e.g. SWISS-MODEL (structure homology-modeling)
ProtParam (protein physical and chemical parameters like theoretical pI and MW)
- Clustal Omega: Server for multiple sequence alignment with some customisation parameters.
- DALI server: Network service for structural comparison of a 3D structure with entries in the protein data bank.
- ESPript: Individual rendering of sequence information, alignments and secondary structure.
- TM-score/TM-align: Assess the quality of protein models and compare topologies.
- PDBePISA: Analysis of assemblies, physical and chemical properties and mapping of interfaces.
- STRIDE: Database-derived recognition and verification of secondary structure from atomic coordinates.
- ConSurf Server: Prediction of functional regions in proteins according to a database.
- PDB2PQR: Tool for Poisson-Boltzmann electrostatics calculations.
- APBS (Adaptive Poisson-Boltzmann Solver): Might be used to compute the surface electrostatics of a protein.
- PDBsum: An EMBL-EBI tool providing a compact pictorial overview of structural characteristics of a given protein in a pdb-file.
- ProCKSI (Protein (Structure) Comparison, Knowledge, Similarity and Information): Detailed comparison and grouping of protein models, further supported by literature data bases.