The Protein Data Bank Through Microsoft Windows. Analyze 3D structure of biological macromolecules fast and easy. WPDB Database Loader help you 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.

WPDB Database Loader Features:
Scientific:
1. Find structures based on text and sequences searches (mismatches allowed).
2. Sequence alignment of one register sequence against multiple target sequences according to the method of Needleman and Wunsch (JMB 48(3): 443-453, 1970).
3. Structure superposition using Calpha positions according to the method of Hendrickson (Acta Cryst. A35:158-163, 1979 .
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 (JMB 55:379-400, 1971) 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. Typical 3-D viewing and rendering, including options to display or highlight substructures, CPK representation, stereo, and simple surfaces (colored based on distance from user).
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. 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.
3. Direct access to Raswin the popular molecular display program.
4. Synchronized printed documentation and context sensitive help created using the DocToHelp package.

Typical Uses
1. Analysis of protein-protein and protein-ligand interactions.
2. Analysis of internal interactions in proteins to reveal different folds (e.g. helix-helix hydrophobic stacking).
3. Analysis of sequence-structure correlation's using sequence search and static property profiles.
4. As above with sequence homology and structure superposition.
5. Analysis of thermal motion using dynamic property profiles.
6. Locate structures based on string searches of combinations of PDB record types and/or sequence patterns.
7. Basic molecular rendering.
8. Basic geometry checking.

Please Note: this program can not support Windows 7/Vista (64-bit).

The license of this software is Freeware, you can free download and free use this graphing software.