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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
haddockHADDOCK (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 >>
Note: The default HADDOCK server is now version 2.2. The previous version (2.1) is still available here (and its grid-enabled version here.)
Note: The regular HADDOCK server might busy at times and/or closed to users because of workshops, tutorials or CAPRI runs. The Grid-enabled version of the HADDOCK server remains however always open. It does require separate registration.
RMSD-based clustering of complexes can be slow and is inadequate for large multi-molecular complexes, particularly when their components are symmetric. We developed a novel clustering strategy that is based on a very efficient similarity measure - the fraction of common contacts. | Read more>>
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
whiscyWHat 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
3ddartThe 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
1A73You 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
7CEIWe present a protein-protein binding affinity benchmark consisting of binding constants (Kda's) for 81 complexes. | Go to service >>

SQUEEZE: The optimal solution for molecular simulations
SQUEEZE is a method to reduce the computational cost of simulations of macromolecules performed under periodic boundary conditions. SQUEEZing allows removing the superfluous solvent molecules, by using the shape of the solute as the basis for the unit cell. This unit cell follows from the optimal packing of the solute, which takes only a few minutes to calculate. The reduction in volume is 50% on average, with respect to a rhombic dodecahedron, depending on the shape of the solute. For near spherical solutes the gain is less, while for some molecules the decrease in volume may be as much as 80%. | Go to service >>