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This web based application enables automation of common functions applied to PDB files before virtual experimentation such as protein-ligand docking. The Scientific Vector Language (SVL) has been implemented in MOE, the Molecular Operating Environment released by the Chemical Computing Group. WebPDB will add Hydrogens, remove heteroatoms and ligands, correct and add missing residues through homology modeling with it's FASTA sequence, and energy minimize your protein. A water accessible surface can also be generated.


The PDB file will be downloaded from the RCSB Protein Data Bank if you provide the PBD ID or you can provide your own pdb file. If upload your own pdb file and select the homology model option then the corresponding pdb id or FASTA sequence file will be required.

A tutorial for this code can be found here

Function and Refinement Options. Default function refinements are pre-selected.
Remove Heteroatoms
  Sensitivity to Non-Standard Residues and Heteroatoms
Defragment Chains
  Heteroatoms must be removed for successful chain defragmentation.
Homology Model
  No Heteroatoms and No fragmented chains.
Environment pH  
Energy Minimize
  Pin Side Chains Side Chain Weight
Surface Creation
  Tightness Probe Radius

Choose a PDB file available through the RCSB Protein Data Bank
Enter PDB ID
Provide your own PDB file with corresponding FASTA sequence text file
Corresponding FASTA File

Check Status of an Existing Job

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