HOMCOS : Searching and Modeling of 3D Structures of Complexes

Searching Contact Molecules for Query Protein

Searching Contact Molecules for Query Protein

This is the service for searching contact molecules with similar proteins to a given query sequence

• Overview of the search
  A user can input a single query protein. The server performs a sequence homology search (blastp; Altschul et al., 1997) with the given query protein sequence for all of the sequences in the PDB(unitmols), to make the list of the homologous proteins. The molecules contacting these homologous unitmol proteins are obtained by searching the contact table, and they are regarded as predicted contacting molecules with the query proteins. These results can be summarized in two ways: Summary Bars and Site Table.

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• Input a query protein sequence
  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.

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• Search results
  The search result can be summarized by the "Bars" view or "Site Table" view. The "Bars" view shows aligned regions of homologous structure as a colored-bar under the horizontal bar of the query sequence. We parepare two types of "Bars" view: "Summary Bars" and "Full Bars". The "Summary Bars" view shows only representative homologous structure, but the "Full Bars" show all of the homologou structure. The "Site Table" view summarizes the results as "one site for one row" format. These three views can be switched by following icons on the top of the window.

  	Summary Bars	Full Bars	Site Table
  Icons on the page top
  Descriptions	Showiing aligned regions of homologous structure as a colored-bar under the horizontal bar of the query sequence. Showing only representative homologous structure.	Showiing aligned regions of homologous structure as a colored-bar under the horizontal bar of the query sequence. Showing all the homologous structure.	Summary as "one site for one row" format.
  Examples of the query PPARD_HUMAN

  On the top of the windows, some common links and tables are shown among the three views.

  • :if you click these numbers, you can change threshold sequence identity for choosing homologues.
  • :if you click these links, you can download the result as a TSV format file. Sreadsheet programs (such as EXCEL) can read it.
  • :If you click (plain), then a BLAST file for PDB is shown in a plain text. If you click (bars), then, it is shown in bar-style.
  • :If you click (plain), then a BLAST file for UniProt is shown in a plain text. If you click (bars), then, it is shown in bar-style. If you click (multiple alignment), then it is shown in multiple alignment-style. If you click (PSSM file), then, a position specific score matrix file is shown.

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• "Summary Bars" view
  We will explain about the "Summary Bars" and "Full Bars" view in more details. Many bars are shown in the left of the window. The width of the bars corresponds to the length of the query protein.
  At the top of the page, the UniProt feature tables are shown in bars, such as domains, motifs, a signal sequence, transmembrane helices.
  In the "MONOMER" section, homologous monomeric 3D structures are shown in bars. Aligned regions are colored by their seconday structures (red: alpha-helices, yellow: beta-strands).
  

  The homologous complexes are classified into seven classes: "HETERO", "NUCLEOTIDE", "COMPOUND", "METAL", "OTHERPOLY", "HOMO", PRECIPITANT"".

  Aligned regions are shown in gray bars, and residue contacting the other molecule are shown in small red boxes.

  If you click 3D icon, 3D structure will be displayed. Details of the 3D model viewer is described in another help page.

  The column "contact_mol" in the middle of the table shows contacting molecules with query's homologues. The column "homologue" shows a homologous protein with the query. In the column "identity[%]", two sequence identities are shown, such as "92.3/72.3". The first number is the sequence identity of the contact site, and the second number is the identiy of all the aligned residues. The identity of the contact sites is a good measure for the qualit of the model, especially for the small chemical compound. In the column "Ncon", two number of contacting residues are shown, such as "13/13". The first number is the number of contact in the aligned regions, the second number is the number of contact sites in all the template sites. If the first number is much smaller than the second, the model can be built by a quite small part of the template complex 3D structures.

  
  
  
  
  

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• "Site Table" view
  The "Site Table" view shows the information about the "searching contact molecules for query protein" in the "one site for one row" table format.　This table is designed for analyzing the effects of amino acid mutations on the structure and the function. It is also useful to analyze disease-associated mutations. A following figure is a snapshot of the "Site Table" view for the sequence PPARD_HUMAN. Columns in the table show following information.

    [n]:site number of query sequence.  [a]:amino acid of query sequence.  [s]:predicted secondary structure from homologous structure."H":alpha-helix, "E":beta-strand, "T":turn.
    [e]:predicted solvent accessible state. "e":exposed, "b":buried [acc]:predicted relative accesssibility[%].  [pdb]:PDB code of homologous structure.
    [contact_mols]:binding other molecules  [observed aa]:Observed amino acids among homologous sequences.  [feature table]:UniProt Feature Table
    [variant]:UniProt Human Variant.
  

  If you click the icon in the left column, the summary page of the specific site appears.A following page is the summary of the 223-rd site of PPARD_HUMAN. "Percentages of Amino Acids in Homologous Proteins" are calcualated by PSI-BLAST from homologues found in UniProt. A mutation to amino acids with less percentage more likely leads to a more severe effect on phenotype. If you click the icon , a following multiple alignment is shown about only the neighbor sites around the focused sites. Among the features in "3D Structual Information", accessibility is reportedly the most important to predict disease-associated mutations, as mutations in buried sites (solvent accessible state="b", or low relative solvent accessibility)　in a protein structure are more likely to lead to unstable states　and to disease.

  If you click the icon in "Templates for 3D complexes"、a following 3D model page is shown for the 3D complex model where the focused site contacts to other molecule.

  We will explain how to use 3D model viewer in another help page.