Tools & Links
Crystallography
The primary mission of TCSB is to enable and take part in the training and development of Structural Biology research at Technion. Toward this goal, the center offers both Expertise and high-end Infrastructure for high-resolution macromolecular crystallography research to zoom in on Biology at the atomic level.
- Promotes international cooperation in crystallography
- Contributes to all aspects of crystallography
- Promotes international publication of crystallographic research
- Facilitates standardization of methods, units, nomenclatures and symbols
- Forms a focus for the relations of crystallography to other sciences
Providing access and tools for exploration, visualization, and analysis of:
- Experimentally-determined 3D structures from the Protein Data Bank (PDB) archive
- Computed Structure Models (CSM) from AlphaFold DB and ModelArchive
These data can be explored in context of external annotations providing a structural view of biology.
Software for Macromolecular X-Ray Crystallography
A comprehensive software package for macromolecular structure determination using crystallographic (X-ray, neutron and electron) and electron cryo-microscopy data.
Chemistry
The Faculty’s research and teaching programs span the full spectrum of disciplines within the chemical sciences, including physical, analytical, inorganic, organic, biochemical and theoretical fields, and maintain strong collaborations with the associated sciences of physics, materials science, biology, biotechnology, nanotechnology and medicine.
State-of-the-art research is a vital part of our academic life. In addition to advancing science and technology, it is a vital tool in the education of our about_faculty-smallundergraduate and graduate students.
Photosynthesis
International Annual Congresses in Asia, Europe & The Americas
Servers
Protein Homology/analogY Recognition Engine V 2.0
Versatile annotation and high quality visualization of macromolecular structures
The Protein Model Portal was developed as a module of the Protein Structure Initiative Knowledgebase (PSI KB). The goal of the Models Module was to develop a portal that gave access to the various models that can be leveraged from PSI targets and other experimental protein structures. The Protein Structure Initiative has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Experimental structural biology and homology modeling thereby complement each other in the exploration of the protein structure space.
Protein structures of UniProt sequences (updated weekly for select core species)
Database of Comparative Protein Structure Models
An open, collaborative consortium for integration and enrichment of 3D-structure data and functional annotations to enable basic and translational research
Compare the performance of several protein modelling services:
- 3D – Protein Structure
- QE – Model Quality Estimation
- QE – Model Quality Estimation
CAMEO continuously applies quality assessment criteria established by the protein structure prediction community. Since the accuracy requirements for different scientific applications vary, there is no “one fits all” score. CAMEO therefore offers a variety of scores – assessing different aspects of a prediction (coverage, local accuracy, completeness, etc.) to reflect these requirements.
Curated protein models with stable links (with DOI).
Since 2006, only structures that have been determined experimentally are allowed to be deposited in the PDB, and theoretical models of macromolecular structures are no longer part of the PDB archive (Berman et al, 2006). ModelArchive is being developed following a community recommendation during a workshop on applications of protein models in biomedical research (Schwede et al, 2009).
ModelArchive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in the corresponding manuscripts. Besides of the actual model coordinates, archiving of models should include sufficient details about assumptions, parameters and constraints applied in the simulation to allow the user of a model to assess and if necessary reproduce the simulation.
See here for a description of the deposition workflow and guidelines on data to be provided.
The development of ModelArchive is supported by the SIB – Swiss Institute of Bioinformatics.
Educational resource about protein structure modeling
Getting a structure for a protein of interest
Exploring protein domains and functional sites
Predicting the effect of mutation on protein function
