ConCavity

Ligand binding site prediction from protein sequence and structure

This webpage provides tools, data, and source code in support of the paper:

Capra JA, Laskowski RA, Thornton JM, Singh M*, and Funkhouser TA*(2009) Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. PLoS Comput Biol, 5(12). [Paper] [Supplementary Text]

Please cite the paper if you use any of the resources below.

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Quick Predict

PDB ID: (e.g. 1g6c)    

Note that predictions are made on the quaternary structures predicted by PQS for each PDB file.

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Resources

• Ligand Binding Site Predictions
  ConCavity's predictions of the ligand binding pockets and residues for structures from the Protein Quaternary Structure database. Visualizations and score files are available for each structure. Due to oddities in the PQS/PDB, predictions are not available for a small number of structures. Please let us know if you need predictions for a missing structure.

• Sequence Conservation Files
  Pre-computed sequence conservation files are available for each structure in the PQS structure database. The conservation scores were computed using the Jensen-Shannon divergence method on the HSSP alignments.

Source Code

• ConCavity v0.1 (updated: 12/18/10)
  This archive contains the C++ source code for ConCavity. See the README for documentation and usage examples. The program is free and licensed under the GNU General Public License (GPL); see the official GNU website for more information.

Supplementary Material

• Supplementary Text
  Additional results and discussion. [PDF]

• Prediction Images and Visualizations
  Ligand binding site predictions of methods described in paper on the LigASite holo dataset. Tarballs coming soon.