193

Task 13.8

Using the DrumPID database: How do I actually find out whether a protein is hit by a drug

or proteins that match a drug effect? This can be investigated using databases such as

DrumPID (Uni Würzburg) or STITCH (EMBL, Heidelberg). Find these databases on

the net.

Task 13.9

Identify papers on natural computing from PubMed.

Task 13.10

A light-targeted protein domain gives a protein new properties. How do you go about

designing it?

Useful Tools and Web Links

NCBI Domains/

Structures

https://www.ncbi.nlm.nih.gov/guide/domains-­structures/

NCBI proteins

https://www.ncbi.nlm.nih.gov/protein

TESS

https://www.cbil.upenn.edu/tess/

Genomatix

https://www.genomatix.de/

TRANSFAC

https://www.gene-­regulation.com/pub/databases.html

MotifMap

https://motifmap.igb.uci.edu/

RNAAnalyzer

https://rnaanalyzer.bioapps.biozentrum.uni-­wuerzburg.de

ICANN

https://www.icann.org

GoSynthetic

https://gosyn.bioapps.biozentrum.uni-­wuerzburg.de/index.php

DrumPID

https://drumpid.bioapps.biozentrum.uni-­wuerzburg.de/

compounds/index.php

BioBricks

https://biobricks.org/

UniProt

https://www.uniprot.org/

SMART

https://smart.embl-­heidelberg.de/

RasMol

https://www.openrasmol.org/

PDB

https://www.rcsb.org/pdb/home/home.do

JASPAR

https://jaspar.genereg.net/

Literature

Adleman LM (1994) Molecular computation of solutions to combinatorial problems. Science

266(5187):1021–1024. (PubMed PMID: 7973651 *Great first work, showing that you can solve

NP problems like the traveling salesman for six cities by gluing DNA rods together [ligation

reactions]. But after that there was a break in “natural computing”.)

Bencurova E, Shityakov S, Schaack D, Kaltdorf M, Sarukhanyan E, Hilgarth A, Rath C, Montenegro

S, Roth G, Lopez D, Dandekar T. (2022) Nanocellulose Composites as Smart Devices With

Chassis, Light-Directed DNA Storage, Engineered Electronic Properties, and Chip Integration.

Front Bioeng Biotechnol. 10:869111. https://doi.org/10.3389/fbioe.2022.869111.

Literature