Only proteins with experimentally determined epitopes Only proteins with experimentally determined active sites Only proteins with sequence features (SOP) SEARCH TYPE Search for protein structure files Enter PDB ID INCLUDE Start to type strain to get suggestions Deselect All Species: Dengue virus Select All (0/10983 strains selected) (6 Types - 3274 complete genomes) Type: Dengue virus (unclassified) Select All (0/646 strains selected) (646 Strains - 54 complete genomes) Type: Dengue virus 1 Select All (0/3106 strains selected) (3106 Strains - 1388 complete genomes) Type: Dengue virus 2 Select All (0/3609 strains selected) (3609 Strains - 999 complete genomes) Select All (0/2842 strains selected) (2842 Strains 700 complete genomes) SELECT VIRUS(ES) TO INCLUDE IN SEARCH Exclude partially sequenced genomes Jump to strain in taxonomy: ADVANCED OPTIONS Remove Select Advanced Option Select An Advanced Option DESCRIPTION KEYWORD Separate multiple keywords by a comma e.g. nmr, crystal Remove Select Advanced Option Select An Advanced Option All PUBLIC DATABASE IDENTIFIER AAA42962.1 e.g. AAA42962.1 Separate multiple IDs by a comma and specify "All" if different types of identifiers are entered. Select Advanced Option Select An Advanced Option Select/Deselect All PDB ID Description UniProt ID Protein Strain Species Name CHOOSE WHICH DATA FIELDS TO DISPLAY IN RESULT DISPLAY FIELDS Remove Select Advanced Option Author AUTHOR Separate multiple author(s) by a comma e.g. M.P.EGLOFF, D.BENARROCH Tip: To select multiple or deselect, Ctrl-click (Windows) or Cmd-click (MacOS) Show All 3D Protein Structure Search Search for 3D protein structure files obtained from the Protein Data Bank (PDB). Protein(s) are associated with each PDB file UniProt database. One protein structure can be assigned to multiple GenBank protein records. 14 matching results Home 3D Protein Structure Search Dengue SEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HOME ViPR is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute and Vecna Technologies. Comments, questions, suggestions? Contact us at [email protected]http://www.viprbrc.org/ Freely available Integrated datasets Bioinformatics tool suite 1 • Search and visualize experimentally determined protein structures in 3D • Highlight ligands, residue, epitopes, or sequence features (regions of viral proteins with specific functional, structural, or immune epitope properties, etc.) on the structure • Download highlighted protein structure image or 3D protein structure movie 3D Protein Structure Visualization On the ViPR homepage, choose a virus family to start. 1. Mouse-over “Search Data” and click “3D Protein Structures”. 2. Search for protein structures of interest using one of the Search Types: • Search for protein structure files: This will retrieve a list of protein structures matching selected search criteria; • Enter PDB ID: Search protein structures by PDB ID. Select or enter in search criteria and click “Search” to run your search. Note that ViPR shows the instant count of search results at the top-right corner of the page to help you search quickly and efficiently. When you select search criteria on search pages, you will instantly know how many records match your search criteria without clicking the “Search” button and actually running the search. Click “Advanced Options” to display additional search fields Retrieve all virus protein structures with a specific public database identifier. Ex., GenBank Accession number AAA42962.1 Select virus types Search by structure authors Search structures by PDB ID Options to limit search results to protein structures with certain data types Instant count of search results Search Clear 2 Dengue 2 virus envelope glycoprotein in the postfusion conformation (PDB ID: 1OK8) Search for 3D protein structures
2
Embed
3D Protein Structure Visualization - ViPR · structure • Download highlighted protein structure imageor 3D protein structure movie D 3D Protein Structure Visualization On the ViPR
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Only proteins with experimentallydetermined epitopes
Only proteins with experimentallydetermined active sites
Only proteins with sequence features(SOP)
SEARCH TYPE Search for protein structure files
Enter PDB ID
INCLUDEStart to type strain to get suggestions Deselect All
SELECT VIRUS(ES) TO INCLUDE IN SEARCHExclude partially sequenced genomes
Jump to strain in taxonomy:
ADVANCED OPTIONS
RemoveSelect Advanced Option
Select An Advanced OptionDESCRIPTION KEYWORD
Separate multiple keywords by a comma
e.g. nmr, crystal
RemoveSelect Advanced Option
Select An Advanced Option All
PUBLIC DATABASE IDENTIFIERAAA42962.1
e.g. AAA42962.1
Separate multiple IDs by a comma and specify "All" if different types of identifiers are entered.
RemoveSelect Advanced Option
Select An Advanced Option
Select/Deselect All
PDB IDDescriptionUniProt IDProteinStrainSpecies Name
CHOOSE WHICH DATA FIELDS TO DISPLAY IN RESULT
DISPLAY FIELDS
RemoveSelect Advanced Option
AuthorAUTHOR
Separate multiple author(s) by a comma
e.g. M.P.EGLOFF, D.BENARROCH
Tip: To select multiple or deselect, Ctrl-click (Windows) or Cmd-click (MacOS) Show All
Add Another Advanced Option
3D Protein Structure Search Search for 3D protein structure files obtained from the Protein Data Bank (PDB). Protein(s) are associated with each PDB file UniProt database. One protein structure can beassigned to multiple GenBank protein records.
14 matching results
Home 3D Protein Structure Search
DengueSEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HOME
About Us Community Announcements Links Resources Support Workbench Sign In
ViPR is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute and Vecna Technologies. Comments, questions, suggestions? Contact us at [email protected]
http://www.viprbrc.org/
Freely available Integrated datasets Bioinformatics tool suite
1
• Search and visualize experimentally determined protein structures in 3D • Highlight ligands, residue, epitopes, or sequence features (regions of viral proteins
with specific functional, structural, or immune epitope properties, etc.) on the structure
• Download highlighted protein structure image or 3D protein structure movie
3D Protein Structure Visualization
On the ViPR homepage, choose a virus family to start.
1. Mouse-over “Search Data” and click “3D Protein Structures”.
2. Search for protein structures of interest using one of the Search Types: • Search for protein structure files: This will retrieve a
list of protein structures matching selected search criteria;
• Enter PDB ID: Search protein structures by PDB ID. Select or enter in search criteria and click “Search” to run your search. Note that ViPR shows the instant count of search results at the top-right corner of the page to help you search quickly and efficiently. When you select search criteria on search pages, you will instantly know how many records match your search criteria without clicking the “Search” button and actually running the search.
Click “Advanced Options” to display
additional search fields
Retrieve all virus protein structures with a specific public database identifier. Ex., GenBank Accession number AAA42962.1
Select virus types
Search by structure authors
Search structures by
PDB ID
Options to limit search results to protein structures with certain data
types
Instant count of search results
Cite ViPR Tutorials Report a Bug Request Web Training Contact Us Release Date: Jun 3, 2012
This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between NorthropGrumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library, Wellcome Images, U.S.Department of Veterans Affairs , Science of the Invisible and ViralZone, Swiss Institute of Bioinformatics.
SearchClear
2
Dengue 2 virus envelope glycoprotein in the postfusion conformation (PDB ID: 1OK8)
Search for 3D protein structures
2
Cite ViPR Tutorials Report a Bug Request Web Training Contact Us Release Date: Jun 29, 2012
This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between NorthropGrumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library, Wellcome Images, U.S.Department of Veterans Affairs , Science of the Invisible and ViralZone, Swiss Institute of Bioinformatics.
Reset View Save View As Image
Type JMol command here. Run
Show JMol Console
Generate Video
Description: CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS ENVELOPEGLYCOPROTEIN IN THE POSTFUSION CONFORMATION
PDB Link: 1OK8
JMOL COMMAND LINE:Advanced users can enter a JMol command directly using JMol Interactive Script .
SAVE/RESTORE STATE You can save the current state of the image (Display Options, Zoom, Highlight Epitopes,etc.) for later use. Click the Show JMol Console button below, click State, andcopy/paste/save the contents of the upper panel into any text document. When youreopen this PDB file in a later session, you can restore the image to the saved state.Click the Show JMol Console button, paste the text into the lower panel, and clickExecute.
GENERATE 3D MOVIEGenerate a mp4/avi movie, starting with the rendering in above window and rotatingaround Y axis by 360 deg. It takes about 30 seconds to generate the movie.
Display Type: Secondary Structure in Cartoon
Details
Highlight Clear
structural Clear
Color Structure By:
Label:
DISPLAY OPTIONS:These options control the general appearance of the protein structure inthe viewer.
HIGHLIGHT LIGANDS Highlight Ligands in
HIGHLIGHT BY SWISS-PROT POSITION Highlight in in this structure corresponding to defined SwissProt
positions. With the dropdown, select a chain and view the positions presentin this file. Enter one or more comma-delimited positions (15,30) or a range(15-30) then click Highlight. If no chain is selected, these positions will behighlighted on all chains which include them.
Select Chain:
A - P12823 (281 - 674) 617-624
PDB Sequence/Structure Details
HIGHLIGHT SEQUENCE FEATURESHighlight sequence features on the structures in . A disabled
checkbox means the mapping between swissprot and pdb position is notcurrently available.
Sequence Feature Feature Name SequenceFeaturePositions
HIGHLIGHT/LABEL FEATURESThese options color, highlight or label certain features of the structure.
DengueSEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HOME
About Us Community Announcements Links Resources Support Workbench Sign In
http://www.viprbrc.org/
Freely available Integrated datasets Bioinformatics tool suite
ViPR is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute and Vecna Technologies. Comments, questions, suggestions? Contact us at [email protected]
3 3. On the search result page, you can: • Click “View Structure” next to the structure
name to load the structure viewing window. • Click “Search Criteria” to revise your selected
search criteria and run another search. • Click “Display Settings” to select display
fields, change the number of records per page, or custom-sort records.
• Download structure records by checking the checkboxes next to the desired records and clicking the “Download” button located above the table.
• Save the search criteria to your personal Workbench account, which is a free service provided to ViPR users. You will be able to rerun the search later.
Visualize and highlight 3D protein structures
Save a publication quality structure image
with highlighted features
• Select display fields • Custom-sort records
Click “View Structure” to display the
selected structure
Download selected records
Save your search criteria to your Workbench space. You will be able to rerun the search later.
4. On the protein structure page, you can rotate and zoom in/out the structure as needed. To the right of the structure, there are many customization options: change display type; highlight ligands, residues, or Sequence Features.
5. Click “Save View as Image” under the structure image to save a publication quality structure image with custom highlights.
Revise your search criteria
Choose from many display options: ball & stick, line, stick, space, charge view, primary structure, secondary structure, etc.
Highlight amino acids using corresponding SwissProt position, with Met as position 1.
Highlight Sequence Features: regions of viral proteins with specific functional, structural, or immune epitope properties, etc. Currently available for Dengue, Hepatitis C, and Vaccinia viruses.