5. Proteína 2D-3D

Secundaria

https://www.predictprotein.org

3D por inteligencia Artifical

     https://www.alphafold.ebi.ac.uk 

3D Basado en Homologa

http://swissmodel.expasy.org/repository/

http://www.rcsb.org/pdb/search/searchSequence.do

SwissModel: https://swissmodel.expasy.org/interactive/

Raptor http://raptorx.uchicago.edu/StructurePrediction/predict/

Phyre http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

M4T server http://manaslu.fiserlab.org/M4T/

3D Ab initio

       Roseta https://yanglab.nankai.edu.cn/trRosetta/

Predicción 3 D de Tasser http://zhanglab.ccmb.med.umich.edu/I-TASSER/

References:

J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8 (2015). (Download the PDF file).

A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738 (2010). (download the PDF file).

Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40 (2008). (download the PDF file).

OTROS

Robetta

http://robetta.bakerlab.org/submit.jsp

Roseta

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

One of AlphaFold’s limitations is that it is not aware of molecules that bind to proteins, which can affect the protein’s 3D structure. Hexokinase (Q96Y14) adopts distinct conformations in the presence (orange, left) and absence (green, right) of sugar. Notably, AlphaFold’s structure prediction aligns with the sugar-free state (as could be seen both visually and via RMSD value).