D3Pockets

Developed by Prof Weiliang Zhu's Laboratory

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Step 1. To set job title

 

Step 2. To select conformation files

MD trajectory(AMBER)   MD trajectory(GROMACS)   Conformational ensemble   PDB

 

Note:

Description of static pocket properties that can be calculated by D3pockets
recfile: the file name of protein
pitfile: the file name of each pocket
volume: the volume of each pocket (unit: cubic angstrom)
num_residue: the number of residues
second_H: the number of residues belonging to alpha helix
second_B: the number of residues belonging to beta sheet
asa: relative accessible surface area calculated by dssp (default standard: Sander and Rost 1994 https://doi.org/10.1002/prot.340200303, unit: square angstrom)
residue_depth: the average distance of the atoms of a residue from the solvent accessible surface (unit: angstrom)
hydrophilic: the number of hydrophilic residues
hydrophobic: the number of hydrophobic residues
hydrophobic_half: the number of hydrophobic residues whose depth is more than the half of maximum residue depth
HSE_UP: the total number of neighbor residues in the upper half sphere centered by each pocket residue
HSE_DOWN: the total number of neighbor residues in the lower half sphere centered by each pocket residue
stable: it's not defined in the current version, so the value is always null.
coverage: the fraction of ligand atoms contained in the pocket. if there is no ligand provided , the value will be null.

 

Step 3. To upload the file

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Note:

    1 MD trajectory(AMBER) : The uploaded file should be in a compressed format containing topology file saved as AMBER format "prmtop" and trajectory saved as AMBER trajectory format "mdcrd" with size of less than 50 MB. Sample File 1

    2 MD trajectory(GROMACS) : The uploaded file should be in a compressed format containing topology file saved as format "pdb" and trajectory saved as GROMACS trajectory format "xtc" with size of less than 50 MB. Sample File 2

    3 Conformational ensemble: the conformational ensemble should be generated by the script. Sample File 3

    4 PDB: The protein structure file(pdb file). Sample File 4

    5 If you want to upload larger job, please contact us.