Prediction of protein binding sites is important for the developement of new drugs targeting protein-protein interactions. We show unambiguously for the first time that protein-protein binding sites are structurally conserved. A new algorithm to predict protein-protein binding sites using conservation of both protein surface structure and physical-chemical properties in structurally similar proteins was developed. The predicted binding sites and the actual binding sites are in good agreement. Our algorithm is a useful tool for the prediction of protein binding sites.
We have also developed a web-tool, available at http://probis.cmm.ki.si for protein binding sites detection, which implements methods described in publication above.
We developed new local structural alignment algorithms for prediction of protein-protein binding sites. The search for structural neighbors in the new algorithms has been extended to all the proteins in the PDB and the query protein is compared to more than 60 000 proteins or over 300 000 single-chain structures. The resulting structural similarities are combined and used to predict the protein binding sites. This study shows that the location of protein binding sites can be predicted by comparing only local structural similarities irrespective of general protein folds.
Study of the structure and mechanisms of diaryliodonium salts which bind the active fluorine is important for the design of new active substances to perform positron emission tomography (PET) scans. In this paper we focused on the formation of dimers and their energetics.
We have introduced a generalization of the AdResS method, which allows for changing the spatial resolution on-the-fly during the course of simulation. The generalization, which is based on thermodynamic arguments, ensures a thermodynamic equilibrium among molecules of different representations. The robustness of the algorithm is tested for two examples, i.e., an adaptive resolution simulation for a liquid of tetrahedral molecules and a binary mixture of tetrahedral molecules and spherical solutes.