PepLig Dataset

Here we have provided the dataset of 702 peptide-ligand complexes which have been used to analyse the residue preferences in the peptide-ligand interface. These complexes were collected and compiled from the Protein Data Bank (PDB). [help page]

PepLigDock Dataset

Here we have provided the dataset of 57 peptide-ligand complex on which we have done the benchmarking of seven docking software. These complexes were collected and compiled from the Protein Data Bank (PDB). [help page]

• Crystal Complex: This peptide-ligand complexes were directly dowloaded from the PDB. Receptor of this complex contains only that chain that we have used for the benchmarking study.
• Receptor: Before the benchmarking study, peptide and ligands were separated from the complexes. According to their geometry, there was a need to correct some of them.These corrections were made manually by means of Schrodinger package.
• Crystal ligand: Crystal ligands were separated from peptide-ligand complexes. These are the ligands, which is present in crystallized peptide-ligand complexes, available in PDB.
• Curated Crystal ligand: The ligands were extracted from the peptide-ligand complexes.Then hydrogen atoms were added to the crystal ligands using add hydrogen module of Schrodinger package and corrected errors if any.
• Minimized ligand: These ligands are the energy minimized coordinates. Curated crystal ligands were minimized using GAFF force field in Open Babel and represented here as minimized ligands.
• CCD ligand: There are standard coordinates for chemical compounds are available in library called Chemical Component Dictionary available in PDB. These ligands were represented as CCD ligands.