Protein Similarity Search

Protein Sequence-based Search (BLAST)

Perform the sequence similarity search against the protein structure database.

Protein Structure-based Search (DALI Pair-wise)

Compare two structural folds.

Protein Structure-based Search (DALI database Search)

Perform the structure-based similarity search against the protein structural database.

Protein Structure Validation

Ramachandran Plot

Calculate and visualize the Ramachandran plot for protein structure.

Structural Tools

Assign B-Factor

Assign a B-factor in the uploaded PDB file.

PDB Structure Summary

Functionality to get the number of chains, Bound ligand(s), Mutation, etc.

Structure Selection

Rewrite the PDB file based on the selected chain(s).

Neighbourhood Selection

Calculate the neighbouring contacts given a reference residue and distance cutoff.

Electrostatic Surface

Calculate and visualize the pqr and dx files for the electrostatic surface.

Mutate Protein

Mutate the reference residue with a new specified residue.

Accessible Surface Area

Calculate the ASA using the specified solvent radius.

Structural Analysis

Contact Map

Calculate and visualize residue pairs matrix at a given distance cutoff.

Protein Superimposition

Superimpose and visualize two structural entries.

Protein-ligand Interactions

Calculate and visualize the number and type of interactions between the Protein-ligand complex.

Protein-Protein Interactions

Calculate and visualize the number and type of interactions between the Protein-Protein complex.

Buried Surface Area

Calculate the buried surface area between the interacting protein domains.

Molecular Docking and Screening

Molecular Docking

Calculate and visualize the docking pose at the known protein binding site region.

Structural Ensemble Analysis

RMSD Calculation

Calculate and visualize a time evolution RMSD plot for AMBER trajectory.

Pair-wise RMSD

Calculate and visualize the All vs All RMSD matrix for AMBER trajectory.

RMSF Calculation

Calculate and visualize the average selected atom fluctuation plot for AMBER trajectory.

Residue-residue Distance

Calculate and visualize a time evolution residue-residue distance plot for AMBER trajectory.

Atom-atom Distance

Calculate and visualize a time evolution atom-atom distance plot for AMBER trajectory.

Ramachandran Analysis

Calculate and visualize the Ramachandran Matrix plot for a given residue for AMBER trajectory.

Radius of Gyration

Calculate and visualize a time evolution RoG plot for AMBER trajectory.

Native Contacts

Calculate and visualize a time evolution native contacts plot for AMBER trajectory.

Secondary Structure Analysis

Calculate and visualize a time evolution SS content distribution plot for AMBER trajectory.