Profile >>

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.)
PRODIGY (PROtein binDIng enerGY prediction) webserver predict of the binding affinity in protein-protein complexes. To use PRODIGY you just need to provide the three-dimensional structure of your complex/complexes as PDB/mmCIF format. | Go to service >>
DISVISDISVIS allows you to quantify and visualize the information content of distance restraints between macromolecular complexes. | Go to service >>
POWERFITPOWERFIT allows you to automaticall fit atomic models into cryo-EM density maps. | Go to service >>
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 >>
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>>
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 (Kd’s) for 81 complexes. | Go to service >>