MOTIVATION Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected in the modelling of biomolecular complexes. METHODS We present a solvated docking approach that explicitly accounts for the presence of water in protein-protein complexes. Our solvated docking protocol is based on the concept of the first encounter complex in which a water la...

Intrinsic flexibility of DNA has hampered the development of efficient protein-DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc. 125, 1731-1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimiza...

The function of the swimbladder in fish hearing is well established for the ostariophysine species, which possess a chain of ossicles connecting the swimbladder mechanically to the perilymph of the labyrinth (cf. von Frisch, 1936; Poggendorf, 1952). However, the auditory function of the swimbladder in fish lacking a mechanical connexion between the swimbladder and the ear is less clear. Van Ber...

Insulin hormone is an important part of the endocrine system. It contains two polypeptide chains and plays a pivotal role in regulating carbohydrate metabolism. Insulin receptors (IR) located on cell surface interacts with insulin to control the intake of glucose. Although several studies have tried to clarify the interaction between insulin and its receptor, the mechanism of this interaction r...

Bone deformities are one of the main effects crude oil exposure in marine fish larvae. Craniofacial and jaw deformities, if severe enough, may restrict feeding ultimately kill developing This study aimed to examine impact dispersed on bone development Atlantic haddock ( Melanogrammus aeglefinus ) larvae, a species spawning areas approached for gas exploration North Ocean. larvae were exposed lo...

To improve the health of population, it is necessary to develop products that contain natural ingredients with antioxidant properties. The development technology meat and fish molded semi-finished Ayurvedic direction relevant today. main raw material was poultry meat. After conducting a literary review scientific publications comparing chemical composition different types fish, we selected sea ...

The structure determination of protein-protein complexes is a rather tedious and lengthy process, by both NMR and X-ray crystallography. Several methods based on docking to study protein complexes have also been well developed over the past few years. Most of these approaches are not driven by experimental data but are based on a combination of energetics and shape complementarity. Here, we pre...

We have shown previously that given high-resolution structures of the unbound molecules, structure determination of protein complexes is possible by including biochemical and/or biophysical data as highly ambiguous distance restraints in a docking approach. We applied this method, implemented in the HADDOCK (High Ambiguity Driven DOCKing) package (Dominguez et al., J Am Chem Soc 2003;125:1731-1...

The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long been challenges that prevented the development of efficient protein-DNA docking methods. We have demonstrated the ability our flexible data-driven docking method HADDOCK to deal with these before, by using custom-built DNA structural models. Here we put our method to the test on a set of 47 comp...