Tertiary Structure Analysis

This is collection of freely accessible web tools for the analysis of structural models of proteins. Some of such analyses can be preformed in most of the visualization programs. We included here several standalone structural analysis tools that can run via popular visualization programs.

Multi-purpose Analysis Tools

This set of tools is intended to provide a convenient web interface to simple, commonly used structural biology calculations with PDB files. The calculations includes Ramachandran plots, surface and volume calculations, and hydrogen bonds detection.
WHAT IF is a versatile molecular modeling package. The web interface of this program gives access to some (but many) of its options, including secondary structure , torsion, geometry, surface, contacts and hydrogen bonds analysis.

Motif, Secondary , Super-secondary and Domain Structure

DHcL The server calculates domain structures at different levels of energy hierarchy and elements of the loop-n-lock structure, closed loops and van derWaals locks
Dial Automatic identification of structural domains given the three-dimensional coordinates of a protein.
Domain 3D
Identification of globular domains in protein structure.
Protein Peeling
Protein Peeling is an approach for splitting a protein three 3-D structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.
Secondary structure assignments.

Surface, Pockets and Cavities Analysis

Check also the list of tools for binding pocket prediction.
3D-SURFER Protein surface comparison and analysis
3V Volume and channel calculation
CAVER Identification and visualization of access routes to protein cavities. Available also as standalone program or as PyMOL plugin.
HotPatch Statistical analysis of patches on protein surfaces.
GETAREA Calculation of solvent accessible surface areas, atomic solvation energies and their gradients
MolAxis Identification of molecular channels in proteins
Automatic identification of pockets on protein surface
Determination of the accessible surface area as well as the distance of a residue from the surface of the protein.
Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for PyMOL
Calculations of accessible surfaces areas at atomic (default) and residue (coarse grained) level
SURFs UP Analysis of functional relationships in protein families as inferred from protein surface maps comparison

Sites and Motifs Search

This server allows you to compare a protein structure against the database of 3D template motifs or a structural motif against a database of protein structures.
MultiBind Multiple alignment of protein binding sites. Recognizes spatial chemical binding patterns common to a set of protein structures
PDBeMotif Integrated resource, which provides information about ligands, sequence and structure motifs, their relative position and the neighbor environment. Search criteria can combine sequence motifs, structure motifs, 3D properties (like φ/ψ), secondary structure elements, and protein-ligand interactions.
PESDserv This server allows you to compare surface of lignd bound site against a ligand bound site surface database.
This server allows you to compare a protein structure against a database of patterns or a structural pattern (up to 100 amino acids) against a database of protein structures.
ProSMoS Pattern-based search using interaction matrix representation of protein structures.
RASMOT-3D The server searches the PDB for matches to a user-specified 3D motif .
3-D alignment of binding sites
SuMo allows you to screen the PDB for finding ligand binding sites matching your protein structure or inversely, for finding protein structures matching a given site in your protein.
Superimposé A 3D structural superposition server that include database search engine for protein structures matching for a given site in your protein

Ionization State and Electrostatic Properties

H++ Automated web server that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment.
PBEQ-Solver calculations and visualization the electrostatic potential of your molecule by solving the Poisson-Boltzmann equation (PBE)
PCE Calculation of the electrostatic potentials for a protein by solving numerically the Poisson-Boltzmann equation
PDB2PQR This server enables a user to convert PDB files into PQR files. PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius.
A tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.
PropKa Protein pKa calculations by fast empirical method
webPIPSA Comparison of the electrostatic interaction properties of proteins

Stereochemistry and Geometry

Ramachandran plot
Ramachandran plot analysis.
Ramachandran plot analysis.

Interactions and Contacts

Identify energetically significant cation-pi interactions within proteins
CMA Contact map analysis
CryCo Build the crystal environment of a given PDB file and analyze crystal contacts according to contact surfaces
ESBRI Identify salt bridges within protein and protein complexes
HORI Compute higher order interactions (pairwise interaction, triplet interactions and quadruple interactions) in a protein structure
LPC CSU Automated analysis of interatomic contacts between structural units in the protein structure and between the protein and bound ligands.
PISA Interactive tool for the analysis of macromolecular (protein, DNA/RNA and ligand) interfaces.
Identification of stabilizing residues in proteins


look also in NMA analysis
A program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available
HINGEprot Detects hinge locations using Gaussian Network Model (simplified version of normal modes analysis)
Morph Server
A web-based tool for generating and animating chemically realistic interpolations between two conformations.
TLS Motion Determination analyzes a protein crystal structure for evidence of flexibility. It does this by partitioning the protein chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion.


CALCOM Calculation of molecule center of mass