Proteins @ AGAI
Proteins at AG AI
Life and development of all organisms are mainly determined by molecular interactions, e.g. between DNA and proteins, proteins and proteins, or proteins and small molecules. Among these, protein-protein interactions play an especially important role, like in interactions between antibodies and antigens, receptors and peptide- or protein-hormones, enzymes and substrates or inhibitors. With the growing number of known protein 3D structures predicting whether and where protein molecules interact with each other is becoming of increasing interest. In the cell protein molecules associate spontaneously without the need of external assistance. They form a complex if they exhibit a high affinity to each other, i.e. the free energy of the complex is lower than that of the two single solvated protein molecules. So, given the right methods it should be possible to predict the docking site and orientation of two protein molecules.
The AG AI is engaged in Bioinformatics since 1993.
First approaches to the docking problem at the beginning of the 90ies employed fast correlation techniques. Features used where surface complementarity and some physical-chemical properties. Work had been founded by BMB+F.
Following the Volume approach, we now introduce flexibility into the volume Model. The principle is taken from classic mechanics of deformable bodies. With precomputed elastic parameters the flexibility can be constrained to those surface patches that are known to change their conformation
Knowledge about Side Chain Flexibility is obtained through our own Rotamer Library, which also analyses induced fit conformation changes.
We use additional Information from heuristic Energy Functions on large sets of synthetic Protein conformations.
|sneumann@TechFak.Uni-Bielefeld.DE||Last Update: 18 Dec 02|