Welcome to the Utrecht Biomolecular Interaction Web Portal >>

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

PRODIGY

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

DISVIS

DISVIS allows you to quantify and visualize the information content of distance restraints between macromolecular complexes. | Go to service

POWERFIT

POWERFIT allows you to automaticall fit atomic models into cryo-EM density maps. | 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

FCC CLUSTERING

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

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