1. 1

2. Experimental approaches for structural biology
X-ray crystallography
NMR
cryoEM

3. cryoEM

4. Where to get structural data?
biological molecules
PDB – Protein Data Bank
free
NDB – Nucleic Data Bank
organic molecules
CSD – Cambridge Structural Database
paid

5. PDB History 1957 Myoglobin structure determined 1970’s
Discussions how to establish an archive of protein structures
PDB established at Brookhaven
Oct 1971, 7 structures
1980’s
Technology takes off
molecular biology, instrumentation, computer hardware and software
Number of structures increases
Structural biology is able to focus on medical problems
IUCr requires data deposition to the PDB
1990’s
Complexity of structures increases
Structural genomics begins 5

6. Current state of the PDB
– structures in the PDB archive
8 550 new structures deposited in 2014 so far
Depositions by macromolecule type
92.6 % Proteins ( structures)
2.8 % Nucleic acids (2 769 structures)
4.5 % Protein-nucleic acid complexes (5 143 structures)
Depositions by experimental technique:
88.0% x-ray diffraction ( structures)
11.2% solution NMR ( structures)
0.5% cryo-EM (864 structures)
data z
data as of 6

7. from http://www. pdb. org/pdb/static. do
from - Growth of Released Structures Per Year

8. PDB ID
Each structure in the PDB is represented by a 4 character identifier of the form [0-9][a-z,0-9][a-z,0-9][a-z,0-9]
1B3T

9. Data formats of PDB PDB format, mmCIF (and derived xml PDBML)
Friday, April 14, 2017November 8, 1999
Protein Data Bank
Doolittle Building, Rutgers University
Data formats of PDB
PDB format, mmCIF (and derived xml PDBML)
Dictionary resources at:
mmCIF is the PDB archival format
all data released in all three formats
from Genes to Drugs via PDB 9

10. PDB Format legacy format
Friday, April 14, 2017November 8, 1999
Protein Data Bank
Doolittle Building, Rutgers University
PDB Format
legacy format
fortran-like 80 column-wide
not structured enough to describe complicated 3D objects
its limits have been broken several times
99,999 atoms, 34 (or 58) chains
readable by most programs
from Genes to Drugs via PDB 10

11. model – chain – residue – atom

12. mmCIF language based on community-agreed definitions
allows adding new features and customization
mmCIF categories are easily transformed to database tables
not designed to be read by humans, data should be viewed through programs and databases

13. Pubmed, MEDLINE, Entrez etc.

14. NCBI National Institute of Health (NIH) – U. S. government
National Library of Medicine (NLM)
National Centre for Biotechnology Information (NCBI)

15. NCBI (founded 1988, http://www.ncbi.nlm.nih.gov/)
Genomic sequences - GenBank – open access annotated collection of all available nucleotide sequences, doubles each 18 months (October 2008 – bp), new release every 2 months, accession number (U49845) required upon publication
OMIM – Online Mendelian Inheritance in Man, db of diseases together with their genetic components
PubChem ( – db of small organic molecules, includes the information about their bioacivities
Entrez ( – federated search engine offering unified access to all NCBI databases
federovany znamena, ze prohledava vice db

16. MEDLINE journal citations and abstracts for biomedical literature
since free access to MEDLINE via PubMed.
PubMed - Web-based retrieval system developed by the NCBI at the NLM. It is part of NCBI's Entrez.
PubMed contains
abstracts
links to full-text articles
links to other databases
…and much more

17. What’s in Pubmed Most PubMed records are MEDLINE citations.
citations and author abstracts from approx biomedical journals
diverse topics: microbiology, delivery of health care, nutrition, pharmacology and environmental health.
currently over 19 million references dating back to 1948
new material added Tuesday through Saturday
about 90% records are from English-language sources or have English abstracts
Approximately 79% of the citations are included with the published abstract

18. What’s in Pubmed Pubmed Central (PMC) NCBI Bookshelf
db of free full texts
since 2007 paper funded by NIH must be freely available through PMC no later tha 12 month since publishing
NCBI Bookshelf
free biomedical books (biochemistry, molecular biology, …)