WPDB - The Protein Data Bank through Microsoft Windows v2.1


Last Update Jan. 13, 1997

NEW

What is WPDB

The PDB through windows, or WPDB for short, is a Microsoft Windows 3.1 Windows95 and Windows NT (client and server) based program to interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above.

Table of Contents

  • How to get WPDB
  • Building your own databases
  • Future Directions
  • References
    Last Update: Nov. 08, 1995
    WPDB Developers and Version Information

    WPDB Features

    The features supported by WPDB are divided into 2 categories, those that have scientific merit and those considered to be computationally interesting.

    Scientific:

    1. Limited query to find structures for further study -- based on substrings of PDB record types e.g. HEADER, COMPND or primary protein sequence with limited mismatch capability.
    2. Sequence alignment of one register sequence against multiple target sequences according to the method of Needleman and Wunsch.
    3. Structure superposition using Calpha positions according to the method of Hendrickson.
    4. Secondary structure assignments according to the method of Kabsch and Sander.
    5. Amino acid property profile analysis, both static and dynamic: static according to the values compiled by Bogardt et al.; dynamic, mean exposure according to Lee and Richards and experimental B factors. Profiles for a single polypeptide chain or difference profiles for two aligned polypeptide chains may be examined.
    6. Contact map analysis at different cut-off distances and with different atom groups in contact. Single structures or superimposed structures (difference contact maps) can be examined.
    7. 3-D viewing and rendering with the option to display or highlight defined structural components.
    8. Geometry calculation (bond lengths, bond angles, dihedral angles, close non-bonded contacts) including graphical representation and deviations from small molecule distances.

    Computing:

    1. Data compression -- about a 20-fold reduction in storage over the PDB ASCII file distribution, but with: (i) bibliographic information limited to AUTHOR and JRNL records; (ii) optionally the first or all members of an ensemble of NMR or model structures included; (iii) only the first alternative conformation as defined in the PDB file for parts of a crystal structure with partial occupancies; (iv) atomic coordinates rounded to 2 and not 3 decimal places; (v) no PDB REMARK records.
    2. A modular design -- in future releases subsets of derived data beyond secondary structure and exposure will also be available (possibly on CD-ROM) and optionally loaded and queried.
    3. Interoperable display objects -- when a feature is selected in one display object (e.g. a contact map), all other visible display objects (e.g. 3-D viewer) and those invoked subsequently, are also updated to illustrate that feature.
    4. Hooks to other programs -- other programs can be invoked directly with appropriate parameter passing. In WPDB v2.1 Raswin can be invoked.

      New Features v2.0

      For those of you familiar with WPDB v1.0 here are the new features that have been added since v1.0. If you are new to WPDB then you may skip this section.
      • Comparative structure analysis. This is the singular most important addition. More than one structure may be made part of the View. Tools then operate by choosing from the available View to operate on both a single structure and if applicable multiple structures.
      • The View pull-down menu now offers more options and is referred to as Tools.
      • It is now possible to align the sequences of selected polypeptide chains and subsequently perform a structure superposition.
      • The former viewers (3-D, Profile, and Contact map) have been enhanced to handle aligned sequences and superimposed structures as appropriate.
      • Exposure is now available in two forms (i) absolute exposure based solely on the property of the amino acid (ii) relative exposure based on the position in the structure is optionally computed at database load time as part of the derived information on each structure entity. Publicly available databases include relative exposure.
      • Many smaller changes to the interface have been made based on the suggestions of users and beta testers.

      New Features v2.1

      For those of you familiar with WPDB v2.0 here are the new features that have been added since v2.0. If you are new to WPDB then you may skip this section.
      • A single new item has been added to the Tools pull-down and is called Geometry. Geometry calculates and visualizes a variety of standard geometry for the protein main chain. Features include:
        • Bond lengths - summaries and histogram distributions
        • Bond angles - summaries and histogram distributions
        • Dihedral angles - phi, psi, omega Ramachandran and distributions
        • C alpha chirality - summaries and distributions
        • Non-bonded contacts less than 2.6 Å
      • Geometry works in concert with other tools as was true of v2.0. For example selecting a bar in a histogram distribution will indicate residues in that range. Selecting a residue will highlight it in the 3-D viewer and all other tools.

      Typical Uses

      • Analysis of protein-protein and protein-ligand interactions.
      • Analysis of internal interactions in proteins to reveal different folds (e.g. helix-helix hydrophobic stacking).
      • Analysis of sequence-structure correlations using sequence search and static property profiles.
      • As above with sequence homology and structure superpsoition.
      • Analysis of thermal motion using dynamic property profiles.
      • Locate structures based on string searches of combinations of PDB record types and/or sequence patterns.
      • Basic molecular rendering.

      Example - Comparison of Alpha and Beta Chains in Human Hemoglobin

      Explanation

      At top left (WPDB window) we see that the hemoglobin structure with the PDB code 1BAB has been chosen. A sequence alignment between the A and B chains (Align window) by the method of Needleman and Wunsch (JMB 48(3): 443-453, 1970) reveals a 44% similarity. These aligned structures are then superimposed according to the method of Hendrickson (Acta Cryst. A35:158-163, 1979) based on their Calpha coodinates (3D view window). The Contact map window reveals the interactions at a default cut-off of 7 Å between Calpha atoms. Red indicates intrachain contacts (i.e. contacts with itself) observed in both 1BAB_A and 1BAB_B; green indicates intrachain contacts observed in 1BAB_A only and blue - in 1BAB_B only.

      Explanation

      This shows further details of the interaction between the A and B chains. The Profile window has been zoomed to show the exposure according to Lee and Richards (JMB 55:379-400, 1971) for a segment of the aligned sequences. Red represents both the A and the B chain; blue chain A only; green chain B only. The Contact map window has been zoomed to show the interaction between individual residues. A further click would reveal the specific atoms in contact. The 3D view window shows a solid representation of the molecule in a gray scale where the darker the color the farther the residue from the viewer.

      Example - Searching for Buried Residues in Lysozymes

      Explanation

      The above shows the exposure calculated using the method of Lee and Richards for a particlular lysozyme structure (1_LBA). A group of residues in the region 75-85 are shown to be completely buried. These residues are selected and then displayed in the 3-D Viewer. The 3-D viewer can be used to call Raswin directly which in turn makes those selected residues part of the Raswin set and are shown here presented as a space filling representation.

      Example - Thermal Motion in a Toxic Loop

      Explanation

      Postsynaptic neurotoxins, in this case erabutoxin b, are know to function by binding to the acetylcholine receptor. It is believed that this occurs through the so-called toxic loop. The residues forming this loop are highlighted in the 3-D view and hence in the Contact map. Looking at the B factor profiles for these residues indicates a higher thermal motion at the tip region as one would expect.

      Example - Changes in a Neuraminidase upon Antibody Binding

      Explanation

      Two neuraminidase structures are shown, one complexed with the antibody and one without. Arg 368 is a known mutation site and it can be seen from the stereo 3-D view that this residue shifts significantly to accommodate the binding. The exact details of the shift can be seen in the Contact map.

      Availability

      WPDB is available       via anonymous ftp from rosebud.sdsc.edu in the directory /pub/sdsc/biology/WPDB

      Building Your Own Databases

      The software to build your own databases is available by contacting one of the developers.

      Developers and Version Information 

                  Ilya N. Shindyalov              Philip E. Bourne
 
            shindyal@sdsc.edu               bourne@sdsc.edu


                            Version 2.1

      Futures

      Some of the enhancements that we are working on for v3.0 are as follows. We welcome your input.
      1. 32-bit version
      2. Extended set of derived data all available via a CDROM or parts available having been optionally downloaded to the hard disk.
      3. Single back-end database used by Windows and Unix
      4. Support for surface properties.
      5. Topology
      6. Extended query options.