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Active sites in proteins are usually hydrophobic pockets that involve side chain atoms. It is non-trivial to quantify this rule of thumb. Methods such as [Good ford 1985] or [Miranker 1991] use interaction energies between the receptor and different probes in an attempt to locate energetically favourable sites. Unfortunately, this procedure requires the assignment of proton locations and partial charges to the receptor atoms and this is not always easy. While Vander Waals energies can indicate sterically available regions, the long-range nature of electrostatic potentials makes the interpretation of energy levels difficult.
The purpose is to calculate possible active sites in a receptor from the 3D atomic coordinates of the receptor. Such a calculation is useful for suggesting possible mutations for site-directed mutagenesis experiments or to help determine potential sites for ligand binding in docking calculations or MultiFragment Search
Service offerings:
We Determine Active sites of protein structures. Our extensive experience with a wide range of protein structures allows us to select/recommend the protocols needed to determine the Active site of the protein structure and its analysis. Structure availability is not always ideal, the sequence may be in limited length or may have been collected in sub-optimal conditions. We have successfully modelled many sequences like these, optimizing protocols depending on the situation. Following analysis, we determine affinity and standardization of the model on different platforms.
Our past experiences:
The purpose is to calculate possible active sites in a receptor from the 3D atomic coordinates of the receptor. Such a calculation is useful for suggesting possible mutations for site-directed mutagenesis experiments or to help determine potential sites for ligand binding in docking calculations or MultiFragment Search.
- Determined active sites of various proteins in the process of drug discovery
- Expertise in active site determination of complex proteins
- Used specialized software in active site determination
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