Frequently Asked Questions

Frequently Asked Questions

Q1: There are excellent protein complexes sites such as PDB (http://www.rcsb.pdb.org/). Why do I need another protein complex site such as yours?

A: PDB contains a very large collection of facts related to proteins, including reaction specificity, functional parameters, substrates, products, and inhibitors. It is a relational database integrating proteins related data from a number of sources. Interestingly, these extensive databases provide no information on protein-ligand interactions, and no resource has been developed that permits the systematic study of all interactions involved in ligand binding.

Q2: How can I search for interaction data in PROTEIN COMPLEX site?

A: Search is currently by the PDB ID.There is a search option, similar to the Search Lite option of the RCSB Protein Data Bank (http://www.rcsb.org/pdb/).

Q3: What is the result of a query by PDB ID?

A:The result is a list of conectivities between atom and Heteroatom that are present in the query PDB file ,And thier distances which participates in Protein-Ligand interaction. The user can analyse the interaction specificity.

Q4: My query PDB ID does not exist in the PROTEIN COMPLEX database. What can be the reason?

A:Most likely the specified protein is not an Protein complex. Another possibility is the structure was entered into the PDB after the last update of PROTEIN COMPLEX DATABASE.

Q5:My query did not find any interactions. What happened?

A:The interactions in PROTEIN COMPLEX are based on the Protein-Ligand complexes in the PDB, and hence no interactions are found if such structures are not available.

Q6:What is an enzyme interaction site?

A:The broadly defined binding or interaction site of an Protein means the collection of all amino acid residues that interact with any ligand including substrates, products, cofactors, and inhibitors.

Q7:What are the publicly available softwares for viewing protein structure or interaction?

A:They are as follows : HBPLUS, LIGPLOT, NUCPLOT, PROMOTIF, NACCESS, SURFNET, PROCHECK, THREADER, MEMSAT.