- The Utrecht Biomolecular Interactions software portal provides access to software tools developed in the Computational Structural Biology group / NMR Research Group of Utrecht University with a main focus on the characterization of biomolecular interactions. Please note that this site is in active development.
- HADDOCK Web Docking
HADDOCK (High Ambiguity Driven protein-protein DOCKing)
is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods
in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process.
HADDOCK can deal with a large class of modelling problems including
protein-protein, protein-nucleic acids and protein-ligand complexes. | Go to
service >>
- CPORT
- CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor. CPORT predictions can be used as active and passive residues in HADDOCK, using the prediction interface. | Go to service >>
- WHISCY, Protein-Protein Interface Prediction
WHat Information Does Surface Conservation Yield? WHISCY is a program to predict protein-protein interfaces. It is primarily based on
conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your
protein. | Go to service >>
- 3D-DART, DNA Modeling Server
The 3D-DART server provides a convenient means of generating custom structural models of DNA. The "Custom Build" tool allows you
to generate custom models of nucleic acid structures with full control over structural parameters such as: nucleic acid type, sequence, global and local bend
angles, base-pair and base-pair step parameters and groove width. 3D-DART makes use of the well known DNA analysis software 3DNA | Go to service >>
- Protein-DNA Docking Benchmark
You can put your protein-DNA docking algorithm to the test using our protein-DNA benchmark. The
benchmark contains 47 unbound-unbound test cases of a varying degree of difficulty. The variety in test cases make this non-redundant
benchmark a useful tool for comparison and further development of protein-DNA docking methods. Visit the site to read more and download
the benchmark. | Go to service >>
- Protein-Protein Binding Affinity Benchmark
We present a protein−protein binding affinity benchmark consisting of binding constants (Kd’s)
for 81 complexes. | Go to service >>
- Services
- Our software web portal is an easy gateway for you to use many of the powerful software packages developed in our group. Read a bit more about all the services that we offer and take a peek at the state of the art computer clusters that are running your calculations.
- Learn more >>
- Research
- Research within the computational structural biology group focuses on the development of reliable bioinformatic and computational approaches to predict, model and dissect biomolecular interactions at atomic level. For this, bioinformatic data, structural information and available biochemical or biophysical experimental data are combined to drive the modelling process. By following a holistic approach integrating various experimental information sources with computational structural biology methods we aim at obtaining a comprehensive description of the structural and dynamic landscape of complex biomolecular machines, adding the structural dimension to interaction networks and opening the route to systematic and genome-wide studies of biomolecular interactions.
- Learn more >>
- Acknowledgements
- The continuous development of HADDOCK and its web server is made possible thanks to the financial
support of several national and European grants.
- Learn more >>
- Links:
- NMR Spectroscopy >>
The servers home, the NMR Spectroscopy Department - Bijvoet Center >>
The Bijvoet-Center for structural biology - Faculty of
Science >>
Faculty of Science main page - Utrecht University >>
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- As of 1 June 2008