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.

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.

Research
Services
HADDOCK logo

HADDOCK

HADDOCK is an integrative platform for the modeling of biomolecular complexes. It supports a large variety of input data and can deal multi-component assembles of proteins, peptide, small molecules and nucleic acids.

PRODIGY logo

PRODIGY

PRODIGY predicts the binding affinity of protein-protein and protein-small molecules complexes and also allows to classify crystallographic interfaces as biological or not.

DISVIS logo

DISVIS

DISVIS quantifies and visualizes the information content of distance restraints between two molecules.

POWERFIT logo

POWERFIT

POWERFIT automatically fits atomic models into cryo-EM density maps.

SPOTON logo

SPOTON

SPOTON determines hot-spot residues at protein-protein interfaces.

CPORT logo

CPORT

CPORT is a meta predictor for protein-protein interface residues.

WHISCY logo

WHISCY

WHISCY predicts protein-protein interfaces, based primarily on conservation, but also taking into account structural information.

3D-DART logo

3D-DART

3D-DART builds custom DNA models with specific bend properties.

proABC-2 logo

PROABC-2

proABC-2 predicts which residues of an antibody are forming intermolecular contacts with its cognate antigen.

FCC logo

FCC CLUSTERING

A novel clustering strategy that is based on a very efficient similarity measure - the fraction of common contacts.

PDB-tools logo

PDB-tools

A dependency-free cross-platform Swiss army knife for massaging PDB files.

Benchmarks and Datasets
Protein-DNA Docking Benchmark

Protein-DNA Docking Benchmark

Our protein-DNA benchmark contains 47 unbound-unbound test cases of a varying degree of difficulty. Visit the site to read more and download the benchmark.

Protein-Protein Binding Affinity Benchmark

Protein-Protein Binding Affinity Benchmark

We present a protein−protein binding affinity benchmark consisting of binding constants (Kd’s) for 81 complexes.

SBGrid datasets

HADDOCK models

Access various HADDOCK models datasets from our lab page at SBGrid.

HADDOCK-ready BM5

HADDOCK-ready BM5

Docking benchmark 5 (BM5) - cleaned and ready to use for HADDOCK.

Learn more
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EOSC-hub
BioExcel
EGI-Engage
NWO
This work is co-funded by the Horizon 2020 projects EOSC-hub (grant number 777536) and BioExcel (grant numbers 823830 and 675728)
and by a computing grant from NWO-ENW (project number 2019.053).