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/
Visualizadores 3D
https://www.rcsb.org/docs/additional-resources/molecular-graphics-software
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).