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Protein Structure Analysis

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ICM-Pro provides a direct dynamic link to the Protein Data Bank (PDB). Once you have downloaded a structure you can analyse the structure - flagging problem regions, superimpose multiple structures, analyse distances and electrostatic properties. See below for a list of key protein structure analysis features. Return to Main ICM-Pro Page

Key Protein Structure Analysis Features

Dynamic link to the Protein Data Bank
One click search and download PDB structures.
Search PDB by keyword.
Search PDB by author.
Search PDB by experiment type or resolution.
Search PDB by Uniprot code.
Search PDB by chemical smiles string.
Search PDB by sequence pattern.
Search PDB by sequence homology.
Tabulated PDB data for easy manipulation, sorting and searching.
Read and display all NMR models from a single PDB file in one click.
Automatically display structure occupancy.
One-click to extract PDB sequence.
Find related chains in the PDB.
PDB File Preparation
Automatic but controled detection and fix of PDB problems.
Identification of optimal positions of added polar hydrogens.
Assignment of the most isomeric form of histidine.
Identification of the correct side-chain groups of glutamine and asparagine.
Protein Superposition
Superimpose multiple structures and calculate RMSD.
On the fly graphical superposition.
Superimpose by specific interatomic pairs.
Superimpose by 3D strucure using visible atoms, C-Alpha, backbone or heavy atoms.
Sequence alignment superposition.
Superimpose multiple protein structures by alignment, residue number, exact match and by visible atoms, C-Alpha, backbone or heavy atoms.
Weighted iterative superposition or single global supeposition for multiple proteins.
Calculate Contact Area
Calculate protein-protein (inter/intra) contact area.
Calculate protein-ligand contact area
Display contact residues according to their contact area e.g. thick sticks for highest contact.
Contact areas are tabulated in a fully-interactive clickable table.
Calculate Surface Area
Calculate solvent accessible area of many different selection types.
Surface area is tabulated in a fully-interactive clickable table.
Measure and Display Distances and Angles.
Measure distances between atoms (all to all, intermolecular or intramolecular)..
Measure planar angles.
Measure dihedral angles.
Display and undisplay distances and angles in the graphical user interface.
Ramachandran Plots
Build fully interactive clickable Ramachandran plots.
Tablulate Phi, Psi, Omg angles.
Save Ramachandran plot as a publication-quality image.
Drug Binding Pocket and Cavity Identification
Calculate and display cavities and ligand pockets in a molecular structure
Calculate cavity volume, area and radius.
Display cavity and pocket neighboring atoms.
Volume and area of pockets displayed in fully interactive plot.
References: An et al 1995, Nicola et al 2008
Protein-Protein Interaction Site Prediction
Protein-protein interaction site prediction using the ICM Optimal Docking Area (ODA) method.
Color the protein by protein-protein interaction hotspots.
Tabulate the ODA prediction for each residue in a fully-interactive table.
References: Fernandez-Recio et al 2005
Protein Health
Calculate relative energy of each residue in a protein.
Color selected residues by strain.
Normalized Energy values for each residue are displayed in a fully interactive table.
Normalized Energy values for each residue are displayed in a fully interactive plot.
References: Maiorov and Abagyan 1998
Predict Side Chain Flexibility
Systematically samples rotamers for each residue side-chain and uses the resulting ensemles to evaluate energy-weighted RMSD for every side-chain atom.
Color the structure by side-chain flexibility.
Conformational entropy for each residue side-chain is calculated and stored in a fully-interactive table.
Protein-Ligand Interactions
One click ligand pocket display.
Ligand pocket colored by binding properties.
Ligand surface colored by binding properties.
Color surface by proximity to Molecule.
Dynamic hydrogen bond display.
Display intermolecular hydrogen bonds.
Easy off and on display of hydrogen bonds.
Export hydrogen bond list to table.
Select hydrogen bond atom pairs.
Change the representation of hyrdrogen bonds (e.g. dotted line, spheres, solid line, telescopic, even).
Color hydrogen bond by energy (red strong-->blue weak)
Change the representation of hydrogen bond style based on energy or atom size}
Set the hydrogen bond minimum energy.

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