152

Roche Biochemical

Pathways

https://www.roche.com/sustainability/what_we_do/for_communities_

and_environment/philanthropy/science_education/pathways.htm

ROSETTA

https://www.rosettacommons.org/software/

SCOP

https://scop.mrc-­lmb.cam.ac.uk/scop/ updated latest version at:

https://scop.berkeley.edu; SCOPe (enhanced)

SignalP

https://www.cbs.dtu.dk/services/SignalP/

SMART

https://smart.embl-­heidelberg.de/

SQUAD

https://www.vital-­it.ch/software/SQUAD

STRING

https://string-­db.org/

STITCH

https://stitch.embl.de/

SWISS-MODEL

https://swissmodel.expasy.org

TargetScan

https://www.targetscan.org/vert_71/

TCGA

https://www.cancer.gov/about-­nci/organization/ccg/research/

structural-­genomics/tcga

TESS

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

TMHMM

https://www.cbs.dtu.dk/services/TMHMM/

YANAsquare

https://www.bioinfo.biozentrum.uni-­wuerzburg.de/computing/

yanasquare/

Useful Tools and Web Links     (continued)

Literature

Alberts B (2013) Essential cell biology, 4. Aufl. Garland Sciences (Taylor & Francis Group), United

States (ISBN-13: 978-0815344544, ISBN-10: 0815344546)

Chen Z, Kibler RD, Hunt A et  al (2020) De novo design of protein logic gates. Science

368(6486):78–84. https://doi.org/10.1126/science.aay2790

Dominguez M, Alvarez S, de Lera AR (2017) Natural and structure-based RXR ligand scaf­

folds and their functions. Curr Top Med Chem 17(6):631–662. https://doi.org/10.217

4/1568026616666160617072521

Fuchs M, Kreutzer FP, Kapsner LA et al (2020) Integrative bioinformatic analyses of global tran­

scriptome data decipher novel molecular insights into cardiac anti-fibrotic therapies. Int J Mol

Sci 21(13):4727. https://doi.org/10.3390/ijms21134727

Kaltdorf KV, Schulze K, Helmprobst F et al (2017) FIJI Macro 3D ART VeSElecT: 3D automated

reconstruction tool for vesicle structures of electron tomograms. Comp Biol 13(1):e1005317.

https://doi.org/10.1371/journal.pcbi.1005317

Lam PC, Abagyan R, Totrov M (2018) Ligand-biased ensemble receptor docking (LigBEnD): a

hybrid ligand/receptor structure-based approach. J Comput Aided Mol Des 32(1):187–198.

https://doi.org/10.1007/s10822-­017-­0058-­x

Leman JK, Weitzner BD, Lewis SM et al (2020) Macromolecular modeling and design in Rosetta:

recent methods and frameworks. Nat Methods. https://doi.org/10.1038/s41592-­020-­0848-­2

Mahalapbutr P, Lee VS, Rungrotmongkol T (2020) Binding hot spot and activation mechanism of

maltitol and lactitol towards the human sweet taste receptor. J Agric Food Chem. https://doi.

org/10.1021/acs.jafc.0c02580

11  Design Principles of a Cell