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Information on PLIC Entries

All the general information on the entries present in the database can be downloaded in the tabular file. The file consists of following columns:

• Binding Site ID
• Binding Site Name
• PDB ID
• Chain ID
• Ligand ID
• Ligand Name
• PDB Title
• Resolution
• Protein Name
• Entity ID
• Uniprot ID
• EC Number
• Cath Superfamily ID

PocketMatch Results

All pairwise comparison of scores between the binding sites can be downloaded in the form of tabular file. The file consist of following columns:

• Binding Site 1 ID(Correspondences to be obtained from the file above between the name and ID)
• Binding Site 2 ID
• PocketMatch Min Score (PMIN Score)
• P-Value of PMIN Score
• PocketMatch Max Score(PMAX Score)
• P-Value of PMAX Score
• No. of Distance Elements Matched
• No. of Distance Elements in first binding site
• No. of Distance Elements in second binding site

Binding Site Descriptors

All the descriptors related to binding site present in the database obtained from fpocket algorithm can be downloded as text file. The fields present in the file are as folllows:

• Binding Site ID
• Pocket Volume (cubin angstroms)
• No. of Alpha Spheres
• Mean alpha sphere radius
• Mean alpha sphere solvent accessibility
• Proportion of apolar alpha sphere
• Mean local hydrophobic density
• Hydrophobicity Score
• Volume Score
• Charge Score
• Proportion of Polar Atoms
• Alpha Sphere Density
• Max dist. between centre of mass and alpha sphere
• Max. theoretical shape complementarity
• Observed shape complementarity
• Normalized shape complementarity

Binding Energy components derived from Autodock4.1

• Binding Site ID
• Autodock4.1 Score
• Electrostatic Score
• Hydrogen bond Score
• van der Waal Score
• Desolvation Score
• Torsional Score

Protein Residues in contact with Ligand

Information on all the residues making contacts with the ligand atoms obtained from LPC program can be downloaded as flat file. The different columns present in the file are as follows:

• Binding Site ID
• Protein Residue Number
• Protein Residue Name
• Contact Distance (In angstroms)
• Contact Surface (Square angstroms)
• H-bonds
• Aromatic contacts
• Hydrophobic contacts
• Destabilizing contacts

Atomic contacts with ligands

Information on all the atomic contacts made by the protein with the ligand atoms derived from LPC can be downloaded as flat file. The different columns present in the flat file are as follows:

• Binding Site ID
• Ligand Atom Number
• Ligand Atom Name
• LPC Ligand Atom Type
• Protein Residue Name
• Protein Residue Number
• Protein Atom Name
• LPC Protein Atom Type
• Contact Distance(In angstroms)
• Contact Surface Area(In square angstroms)

Putative Hydrogen bonds between protein and ligand

All the hydrogen bond information between the protein and the ligand can be downloaded as flat file. The different columns names present in the file are :

• Binding Site ID
• Ligand Atom Number
• Ligand Atom Name
• Ligand Atom type
• Protein Residue Name
• Protein Residue Number
• LPC Protein Atom type
• Contact Distance (In angstroms)
• Contact Surface Area (In square angstroms)

Experimental Binding Affinity Values

All the experimental data present for the protein-ligand interactions present in the data obtained from PDB can be downloaded here. The differnet columns present in the database are as follows:

• Binding Site ID
• Binding Site Name
• Ki(nM)
• Kd(nM)
• EC50(nM)
• IC50(nM)
• deltaG(kJ/mol)
• deltaH(kJ/mol)
• -TdeltaS(kJ/mol)
• Ka(1/M)

Information on waters present in binding site

Information present on water present in binding sites making contacts can be downloaded here. The different columns present in the file are as follows:

• Binding Site ID
• Donor Residue
• Donor Chain
• Donor Residue number
• Donor Atom
• Acceptor Residue
• Acceptor Chain
• Acceptor Residue Number
• Acceptor atom
• Distance (In angstrom)

EasyMIFs characterization of binding site

Information on interaction profile of certain probes used - CMET,AR1,OP and OA in the binding site environment can be downloaded as flat file. The different columns present in the file are as follows:

• Binding Site ID
• Methyl probe (CMET) Average Interaction Energy
• Methyl probe Total Interaction Energy
• Methyl probe Total no. of interacting grids
• Total Methyl probe interaction clusters
• Phosphate probe (OP) Average Interaction Energy
• Phosphate probe Total Interaction Energy
• Phosphate probe Total no. of interacting grids
• Total phosphate probe interaction clusters
• Hydroxy probe (OA) Average Interaction Energy
• Hydroxy probe Total Interation Energy
• Hydroxy probe Total no. of interacting grids
• Total Hydroxy probe interaction clusters