ISPMEC stands for Interaction Specificity in Protein Complexe of Metals and Energetic Compounds . It is simple web based tool, which calculates the atomic interactions between Ligand and Protein molecule.
The understanding of noncovalent interactions in protein ligand complexes is essential for
better understanding of the physical nature of molecular recognition and should contribute toward the discovery of new compounds or molecules with desired interaction specificity.
The main objective behind the development of ISPMEC was to have some tool which could provide the detail insight of interaction profile of each ligand associated to the given protein-complexes of metal or energetic compound.
How it works
Upon selecting the given Protein-Ligand Complex, it determines the available ligand types and chains in the selected complex. User can select different options to evaluate the interactions specificity of ligand in the complex. The result table contain the details of each atomic interaction between ligand and protein molecule in the given protein complex.
The interface is self explanatory and it only requires the PDB file containing at least one ligand. In the present tool, two methods have been implemented to analyze interaction specificity. The first method is based upon the connectivity records of the PDB format and the second methods is based upon the user-defined atomic distance (RMSD or Euclidian distance) for particular interaction. User can opt for different level of distance cut-offfor specific ligand and can analyze the interaction alternatives.The connectivity matrix based method calculates faster than RMSD based method.
By setting different cut-off distances, user can easily analyze various covalent and non-covalent interactions such as H-bond, Electrostatic, Van der Waals etc.,
The information on interaction profile of any ligand to its receptor is very useful for scientists working in the area of molecular recognition and further this profiling may be exploited for designing novel ligands with better interaction specificity.