Structure examples

Protein backbone and secondary structure

Assembly of a straight peptide from sequence

Assembly of a straight peptide from sequence

Ramachandran plot of dynein motor domain

Ramachandran plot of dynein motor domain

Determination of amino acid enantiomers

Determination of amino acid enantiomers

Arrangement of beta-sheets

Arrangement of beta-sheets

Three ways to get the secondary structure of a protein

Three ways to get the secondary structure of a protein

Nucleic acid base pairs and secondary structure

Plotting the base pairs of a tRNA-like-structure

Plotting the base pairs of a tRNA-like-structure

Leontis-Westhof Nomenclature

Leontis-Westhof Nomenclature

Comparison of a tRNA-like-structure with a tRNA

Comparison of a tRNA-like-structure with a tRNA

Visualization of Watson-Crick base pairs

Visualization of Watson-Crick base pairs

Small molecules

Enumeration of alkane isomers

Enumeration of alkane isomers

Molecular visualization of a small molecule using Matplotlib

Molecular visualization of a small molecule using Matplotlib

Partial charge distribution

Partial charge distribution

Proximity and contacts

Construction of an adjacency matrix

Construction of an adjacency matrix

Contact sites of protein-DNA interaction

Contact sites of protein-DNA interaction

Detection of disulfide bonds

Detection of disulfide bonds

Hydrogen bonds between protein domains

Hydrogen bonds between protein domains

Identification of lipid bilayer leaflets

Identification of lipid bilayer leaflets

Molecular dynamics and docking

Docking a ligand to a receptor

Docking a ligand to a receptor

Basic analysis of a MD simulation

Basic analysis of a MD simulation

BinaryCIF as trajectory format

BinaryCIF as trajectory format

LDDT for predicted structure evaluation

LDDT for predicted structure evaluation

Visualization of normal modes from an elastic network model

Visualization of normal modes from an elastic network model

Creation of an amino acid rotamer library

Creation of an amino acid rotamer library

Analysis of solvation shells

Analysis of solvation shells

Secondary structure during an MD simulation

Secondary structure during an MD simulation

Cavity solvation in different states of an ion channel

Cavity solvation in different states of an ion channel

Structural alphabets

Multiple Structural alignment of orthologous proteins

Multiple Structural alignment of orthologous proteins

Searching for structural homologs in a protein structure database

Searching for structural homologs in a protein structure database

Miscellaneous

Biological assembly of a structure

Biological assembly of a structure

Calculation of protein diameter

Calculation of protein diameter

Identifying unresolved regions in protein structures

Identifying unresolved regions in protein structures

Visualization of glycosylated amino acids

Visualization of glycosylated amino acids

Superimposition of homologous protein structures

Superimposition of homologous protein structures

Annual releases of PDB structures

Annual releases of PDB structures