Rensselaer Exploratory Center for Cheminformatics Research: Software

Rensselaer Exploratory Center for Cheminformatics Research (RECCR)

WebPDB

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.

Documentation

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.

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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

PDB

Corresponding FASTA File

Check Status of an Existing Job

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