:orphan: Structure examples ================== .. raw:: html
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Protein backbone and secondary structure ---------------------------------------- .. raw:: html
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.. only:: html .. image:: /examples/gallery/structure/protein/images/thumb/sphx_glr_peptide_assembly_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_protein_peptide_assembly.py` .. raw:: html
Assembly of a straight peptide from sequence
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.. only:: html .. image:: /examples/gallery/structure/protein/images/thumb/sphx_glr_ramachandran_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_protein_ramachandran.py` .. raw:: html
Ramachandran plot of dynein motor domain
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.. only:: html .. image:: /examples/gallery/structure/protein/images/thumb/sphx_glr_residue_chirality_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_protein_residue_chirality.py` .. raw:: html
Determination of amino acid enantiomers
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.. only:: html .. image:: /examples/gallery/structure/protein/images/thumb/sphx_glr_sheet_arrangement_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_protein_sheet_arrangement.py` .. raw:: html
Arrangement of beta-sheets
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.. only:: html .. image:: /examples/gallery/structure/protein/images/thumb/sphx_glr_transketolase_sse_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_protein_transketolase_sse.py` .. raw:: html
Three ways to get the secondary structure of a protein
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Nucleic acid base pairs and secondary structure ----------------------------------------------- .. raw:: html
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.. only:: html .. image:: /examples/gallery/structure/nucleotide/images/thumb/sphx_glr_base_pairs_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_nucleotide_base_pairs.py` .. raw:: html
Plotting the base pairs of a tRNA-like-structure
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.. only:: html .. image:: /examples/gallery/structure/nucleotide/images/thumb/sphx_glr_leontis_westhof_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_nucleotide_leontis_westhof.py` .. raw:: html
Leontis-Westhof Nomenclature
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.. only:: html .. image:: /examples/gallery/structure/nucleotide/images/thumb/sphx_glr_transfer_rnas_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_nucleotide_transfer_rnas.py` .. raw:: html
Comparison of a tRNA-like-structure with a tRNA
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.. only:: html .. image:: /examples/gallery/structure/nucleotide/images/thumb/sphx_glr_watson_crick_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_nucleotide_watson_crick.py` .. raw:: html
Visualization of Watson-Crick base pairs
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Small molecules --------------- .. raw:: html
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.. only:: html .. image:: /examples/gallery/structure/molecule/images/thumb/sphx_glr_alkane_isomers_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_molecule_alkane_isomers.py` .. raw:: html
Enumeration of alkane isomers
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.. only:: html .. image:: /examples/gallery/structure/molecule/images/thumb/sphx_glr_molecular_visualization_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_molecule_molecular_visualization.py` .. raw:: html
Molecular visualization of a small molecule using Matplotlib
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.. only:: html .. image:: /examples/gallery/structure/molecule/images/thumb/sphx_glr_peoe_visualization_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_molecule_peoe_visualization.py` .. raw:: html
Partial charge distribution
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Proximity and contacts ---------------------- .. raw:: html
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.. only:: html .. image:: /examples/gallery/structure/contacts/images/thumb/sphx_glr_adjacency_matrix_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_contacts_adjacency_matrix.py` .. raw:: html
Construction of an adjacency matrix
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.. only:: html .. image:: /examples/gallery/structure/contacts/images/thumb/sphx_glr_contact_sites_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_contacts_contact_sites.py` .. raw:: html
Contact sites of protein-DNA interaction
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.. only:: html .. image:: /examples/gallery/structure/contacts/images/thumb/sphx_glr_disulfide_bonds_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_contacts_disulfide_bonds.py` .. raw:: html
Detection of disulfide bonds
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.. only:: html .. image:: /examples/gallery/structure/contacts/images/thumb/sphx_glr_domain_hbonds_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_contacts_domain_hbonds.py` .. raw:: html
Hydrogen bonds between protein domains
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.. only:: html .. image:: /examples/gallery/structure/contacts/images/thumb/sphx_glr_leaflet_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_contacts_leaflet.py` .. raw:: html
Identification of lipid bilayer leaflets
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Molecular dynamics and docking ------------------------------ .. raw:: html
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.. only:: html .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_docking_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_modeling_docking.py` .. raw:: html
Docking a ligand to a receptor
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.. only:: html .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_md_analysis_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_modeling_md_analysis.py` .. raw:: html
Basic analysis of a MD simulation
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.. only:: html .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_mmtf_trajectory_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_modeling_mmtf_trajectory.py` .. raw:: html
BinaryCIF as trajectory format
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.. only:: html .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_normal_modes_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_modeling_normal_modes.py` .. raw:: html
Visualization of normal modes from an elastic network model
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.. only:: html .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_rotamer_library_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_modeling_rotamer_library.py` .. raw:: html
Creation of an amino acid rotamer library
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.. only:: html .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_solvation_shells_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_modeling_solvation_shells.py` .. raw:: html
Analysis of solvation shells
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.. only:: html .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_trajectory_sse_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_modeling_trajectory_sse.py` .. raw:: html
Secondary structure during an MD simulation
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.. only:: html .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_water_exchange_noexec_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_modeling_water_exchange_noexec.py` .. raw:: html
Cavity solvation in different states of an ion channel
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Structural alphabets -------------------- .. raw:: html
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.. only:: html .. image:: /examples/gallery/structure/alphabet/images/thumb/sphx_glr_msa_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_alphabet_msa.py` .. raw:: html
Multiple Structural alignment of orthologous proteins
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.. only:: html .. image:: /examples/gallery/structure/alphabet/images/thumb/sphx_glr_structure_search_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_alphabet_structure_search.py` .. raw:: html
Searching for structural homologs in a protein structure database
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Miscellaneous ------------- .. raw:: html
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.. only:: html .. image:: /examples/gallery/structure/misc/images/thumb/sphx_glr_biological_assembly_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_misc_biological_assembly.py` .. raw:: html
Biological assembly of a structure
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.. only:: html .. image:: /examples/gallery/structure/misc/images/thumb/sphx_glr_diameter_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_misc_diameter.py` .. raw:: html
Calculation of protein diameter
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.. only:: html .. image:: /examples/gallery/structure/misc/images/thumb/sphx_glr_gap_bars_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_misc_gap_bars.py` .. raw:: html
Identifying unresolved regions in protein structures
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.. only:: html .. image:: /examples/gallery/structure/misc/images/thumb/sphx_glr_glycan_visualization_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_misc_glycan_visualization.py` .. raw:: html
Visualization of glycosylated amino acids
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.. only:: html .. image:: /examples/gallery/structure/misc/images/thumb/sphx_glr_homolog_superimposition_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_misc_homolog_superimposition.py` .. raw:: html
Superimposition of homologous protein structures
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.. only:: html .. image:: /examples/gallery/structure/misc/images/thumb/sphx_glr_pdb_statistics_thumb.png :alt: :ref:`sphx_glr_examples_gallery_structure_misc_pdb_statistics.py` .. raw:: html
Annual releases of PDB structures
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.. toctree:: :hidden: :includehidden: /examples/gallery/structure/protein/index.rst /examples/gallery/structure/nucleotide/index.rst /examples/gallery/structure/molecule/index.rst /examples/gallery/structure/contacts/index.rst /examples/gallery/structure/modeling/index.rst /examples/gallery/structure/alphabet/index.rst /examples/gallery/structure/misc/index.rst .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_