Protein-RNA interactions 21.04.2017
Repositories of coordinates and structural information
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Protein Data Bank (PBD)
http://www.wwpdb.org/
The Protein Data Bank archive serves as the single repository of information about the 3D structures
of proteins, nucleic acids, and complex assemblies. The Worldwide PDB (wwPDB) organization
manages the PDB archive and ensures that the PDB is freely and publicly available to the global
community.
PBD mirrors:
(US) http://www.rcsb.org/pdb/home/home.do
The RCSB PDB builds upon the data by creating tools and resources for research and education in
molecular biology, structural biology, computational biology, and beyond.
(Europe) http://www.ebi.ac.uk/pdbe/
PDBe is the European resource for the collection, organisation and dissemination of data on
biological macromolecular structures.
Teaching materials: http://www.ebi.ac.uk/pdbe/training/tutorials
Structure validation: http://www.ebi.ac.uk/pdbe/modval1
(Japan) https://pdbj.org/
Nucleic Acid Database (NDB):
http://ndbserver.rutgers.edu/
The NDB contains information about experimentally-determined nucleic acids and complex
assemblies. Use the NDB to perform searches based on annotations relating to sequence, structure
and function, and to download, analyze, and learn about nucleic acids.
Guide to understanding PDB data:
http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction
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Biological Magnetic Resonance Data Bank (BMRB)
http://www.bmrb.wisc.edu/
A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other
Biomolecules
*NMR data related analysis tools http://www.ebi.ac.uk/pdbe/nmr-resources
EMDataBank
http://www.emdatabank.org/
EMDataBank is a unified global portal for deposition and retrieval of 3DEM density maps, atomic
models, and associated metadata, as well as a resource for news, events, software tools, data
standards, validation methods for the 3DEM community.
*How to search in EMdata https://www.youtube.com/watch?v=aXDK6owQovw&feature=youtu.be
EMPIAR
http://www.ebi.ac.uk/pdbe/emdb/empiar/
EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron
microscopy images. Here, you can browse, upload, and download and reprocess the thousands of
raw, 2D images used to build a 3D structure.
Small angle scattering biological databank (SASBDB)
https://www.sasbdb.org/
Curated repository for small angle scattering data and models. SASBDB is a fully searchable curated
repository of freely accessible and downloadable experimental data, which are deposited together
with the relevant experimental conditions, sample details, derived models and their fits to the data.
About the SAXS data https://www.sasbdb.org/help/
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Software for structure visualisation
LiteMol
http://webchemdev.ncbr.muni.cz/Litemol/
Fast, handles 3D data in the browser
PyMOL
https://www.pymol.org/
The leading software package for customization of 3-D biomolecular images. Using PyMOL, data can
be represented in nearly 20 different ways. Spheres provides a CPK-like view, surface and mesh
provide more volumetric views, lines and sticks put the emphasis on bond connectivity, and ribbon
and cartoon are popular representations for identifying secondary structure and topology.
* PyMOL wiki https://pymolwiki.org/index.php/Main_Page
* PyMOL plugin for PBD annotations https://pymolwiki.org/index.php/PDB_plugin
* PyMOL plugin for SAXS data https://www.embl-hamburg.de/biosaxs/manuals/saspy.html
* PyMOL movie school https://pymolwiki.org/index.php/MovieSchool
UCSF Chimera
https://www.cgl.ucsf.edu/chimera/
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular
structures and related data, including density maps, supramolecular assemblies, sequence
alignments, docking results, trajectories, and conformational ensembles. High-quality images and
animations can be generated. Chimera includes complete documentation and several tutorials, and
can be downloaded free of charge for academic, government, nonprofit, and personal use.
* Chimera ‘wiki’ https://www.cgl.ucsf.edu/chimera/docindex.html
UCSF ChimeraX
https://www.cgl.ucsf.edu/chimerax/
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from
the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use.
Advantages over Chimera: https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html
Jmol
http://jmol.sourceforge.net/
Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry,
biochemistry, physics, and materials science.
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Educational resources
PDB Molecule of the month:
http://pdb101.rcsb.org/motm/motm-by-title
Paper models of molecules:
http://pdb101.rcsb.org/learn/resources/paper_models