Linksammlung Strukturanalyse
Software Links und Tools für die Makromolekulare Strukturanalyse
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/APBS (Adaptive Poisson-Boltzmann Solver): Tools for Poisson-Boltzmann surface electrostatics calculations of macromolecules.
- 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.
Protein modelling
- PMP (Protein Model Portal): Links, examples and help concerning protein modelling.
- I-Tasser: Homology-based protein structure (and function) prediction, input: Primary sequence.
- PHYRE2 (Protein Homology/analogY Recognition Engine V 2.0): Determination of protein features and (homology) modelling.
PHYRE2 investigator (advanced features) - ROSETTA: Software suite for predicting/designing protein structures, folding mechanisms, and protein-protein interactions.
- ModFold (Model Quality Assessment Server): Prediction of the quality of a given 3D structure according to various parameters.
- SiteHound: Web server predicting putative ligand binding sites by using different types of probes and a known high-resolution structure.
- AutoDock:Software suite for automated docking designed to predict how small molecules, such as drug candidates, bind to a receptor of known high-resolution structure.
- Sybyl: A suite of computational software particularly designed for drug development, including visualisation, analysing physical/chemical properties of macromolecules and docking/interaction studies.
Kristallographie
- XtalPred: Prediction of protein crystallisability, determination of chemical parameters of the protein.
- CCP4: Software suite for macromolecular X-ray crystallography: Manuals, tutorials, talks.
- COOT: Graphics program for building, refining and analysing macromolecular models: Tutorials and FAQs.
- Ruppweb, Crystallographic Web Applets: A set of calculation tools related to protein crystallography
- PROCHECK: Validation of the stereochemical quality of protein structures
Darstellung von Biomolekülen
- VMD (Visual Molecular Dynamics): A molecular visualisation program for displaying, animating, and analysing large biomolecular systems.
- UCSF Chimera: An extensible molecular modelling system: Support, tutorials and videos.
- PyMOL: Visualising, modifying and animating molecules and atomic details – links, news, support.
- RasMol: Program for molecular graphics visualisation of macromolecules.
SAS (Small Angle Scattering) und CD-Spektroskopie
- ATSAS: Analysis of SAXS data: Ab-initio modelling, crystal structure vs. structure in solution.
- SAS Portal: Software, News and basic information.
- DICHROWEB: Processing and analysis of CD spectroscopy data.