HOMCOS : Help Page

HOMCOS : Searching and Modeling of 3D Structures of Complexes

Hetero Protein Multimer [Go to Japanese page]

Hetero Protein Multimer Model 3D structure of hetero-multimer for two given sequence using homology-modeling technique.

Overview of the search
This service is for modeling the complex 3D structures of hetero multimers from two query proteins. The server performs two seqnece homology searches (blastp;Altschul et al., 1997) with the two given query protein sequences for all of the unitmol sequneces in the PDB, to make two lists of the homologous proteins. The server then checks if a 3D dimeric or multimeric structure of the homologues exists, in which one of the proteins is homologous to one query protein, and another protein is homologous to the other query protein. If the homologous multimers are found, then they can be used as the template for complex modeling. In contrast to the previous version of HOMCOS, our new server can model not only dimeric structures, but also multimeric structures composed of two different proteins, such as the tetrameric structures of hemoglobin alpha and beta chains.
Input two query protein sequences
You can input a query protein sequence by following various methods.
1. ID for several protein sequnece databases UniProt ID and AC, INSDC protein_id, RefSeq protein_id are available.
  
  database example
  
  UniProt ID CDK3_HUMAN [link]
  
  UniProt AC Q00526 [link]
  
  INSDC protein_id AAV40830.1 [link]
  
  RefSeq protein_id NP_001249.1 [link]
2. amino acid sequence (one letter) For example, "GIVEQCCASVCSLYQLENYCN".
3. PDB_ID + CHAIN_ID For example, PDB_ID="2ins" CHAIN_ID="A".
4. Uploading your PDB file
Notes for input the query sequence
- HOMCOS has no string search services; protein names, gene names and keywords cannot be used as the query. If you know only names and keywords of the protein of your interest, please use other servers, such as UniProt, for string searches to get protein_id or amino acid sequences, before accessing HOMCOS.
- We recommended to use UniProt ID or AC for Human/Mouse/Rat queries. We can quickly show the search results of these sequences, because we precalculate BLAST searches for UniProts for these sequences.
- If 3D structure is assigned as the query, template-based docking is available using the query structure.
Search results

We will show a search result page of the hetero modeling service for the two queries CDK5_HUMAN and CCNB1_HUMAN.
This page summarizes results of two homology searches (blastp) for the two given query proteins A and B. Pale red bars in the left are aligned regions for the query protein A, and pale blue bars in the right are those for the query protein B. Deep red and blue boxes ( and )show contacting residues.
If one of the 3D icons in the left column is clicked, a following 3D model viewer window will be displayed.
We will explain how to use 3D model viewer in another help page.

Comments and Questions to:

database	example
UniProt ID	CDK3_HUMAN [link]
UniProt AC	Q00526 [link]
INSDC protein_id	AAV40830.1 [link]
RefSeq protein_id	NP_001249.1 [link]