Q: What is the CSV format?

CSV stands for Comma Separated Values. The first column has entries to denoted different classes and different families are separated by entries in the second column. The family members are in the third column.

Column Contains Possible Values
1 Entries denoting the protein class that follow EC number
2 Entries denoting protein families "Family. Representative Entry is:"
3 Protein ID 4 character PDB ID, uppercase
4 Ligand Name Space separated list of HET group names
5 Ligand Validity* "valid","invalid"
6 Affinity Measure "IC50", "Kd", "Ka", "Ki"
7 = "="
8 Affinity Value numeric value
9 Affinity Unit "M", "mM", "uM", "nM", "pM", "fM", "M^-1"
10 SMILES string SMILES string line noation

*For definition of valid and invalid please see reference publication.

Q: What are the different third party plugins used?

We have embedded commonly used third-party plugins into the website to increase the functionality: Jmol (an open-source Java viewer for chemical structures in 3D; http://www.jmol.org) is used to view the protein-ligand complex; MarvinView (Marvin 5.12.3, 2013, ChemAxon; http://www.chemaxon.com) is used to view the ligand’s 2D structure, and JChem Base (JChem 6.0.0, 2013, ChemAxon; http://www.chemaxon.com) with MarvinSketch is used for structure-based searching of ligands.

Q: What is Jmol viewer?

Jmol is an interactive web browser applet.
Reference: Jmol an open-source Java viewer for chemical structures in 3D. http://www.jmol.org

Q: Jmol viewer is not running or browser crashes while loading PDB record. What should I check for?

Check the followings:
- Make sure java is properly installed on your system. Test whether Java is working on my computer.
- Make sure Java is enabled in your browser.
- Make sure the exception is set in the Java console.
- Chrome is not using NPAPI plugins - try changing browsers.
- See Oracle FAQ
- Accept the security warning when it appears while loading Jmol.
- Accept the security warning when it appears while executing Jmol commands.
- See Jmol FAQ

Q: Where to get help for using Jmol viewer?

- See Jmol Mouse manual
- Right click on the Jmol viewer for Jmol Menu.
- Learn to use Jmol
- See Jmol FAQ

Q: Why doesn't the ligand appear in the Marvin viewer, it has a name?

- Make sure Java is enabled in your browser.
- Make sure the exception is set in the Java console.
- Chrome is not using NPAPI plugins - try changing browsers.
- See Oracle FAQ
- If the ligand does not have coordinates for all the atoms we do not report its SMILES string.

Q: What is a "biounit"?

The biological unit (biounit) is the functional form of the protein. Check out its definition on the PDBWiki. We provide "corrected" biounit files, where any atoms more than 10 Angstroms from the protein were removed. If a symmetry related molecule was generated and the operation was not applied to the water molecules or ligand, these were rotated in accordance with the symmetry operation.

Q: What is union binding site and how it is calculated?

The union binding sites of a leader is an extended site obtained by combining binding site residues of each member in the 90% seq. similar family. Individual binding sites were calculated using a 4.5 Å distance cutoff around the ligand atoms. To better represent binding sites in their functional environment, biological assemblies (biounits) were used, instead of asymmetric units in PDB. We have used the ProBiS algorithm, in order to create the residue correspondences between leader and family members. These correspondences were used to extend the leader binding site into a union of all family members binding site. ProBiS ref: Konc, J. & Janežič, D.; Bioinformatics 26, 11601168 (2010).

Q: How families based on binding site similarity calculated?

We calculated the binding site similarity for the union_binding_site for all leaders using the APoc program. APoc (Alignment of Pockets), is an efficient program for large-scale structural comparison of protein pockets. We used the default parameters in APoc, which gives p-values and z-scores for each binding site comparison. To extract the statistically significant binding site associations, p-values below 0.05 in APoc was considered. APoc Ref: Gao, M. & Skolnick, J.; Bioinformatics 29, 597604 (2013).

Q: Where to get more Help?

Email us at BindingMOAD@UMich.edu.

Q: How to cite Binding MOAD?
  • Cite Binding MOAD: L Hu, ML Benson, RD Smith, MG Lerner, HA Carlson. Binding MOAD (Mother Of All Databases).Proteins 2005, 60, 333-40.
  • Additional Reference: ML Benson, RD Smith, NA Khazanov, B Dimcheff, J Beaver, P Dresslar, J Nerothin, and HA Carlson. Binding MOAD, A high-quality protein-ligand database. Nucleic Acids Research 2008, 36, D674-D678.

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