Wiki (private)

Jaramillo Lab

Software and resources (licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License):

ProtDes: Computational protein design (fully automated) package macro for CHARMM. Please cite  Suarez, M., Tortosa, P. & Jaramillo, A. PROTDES: CHARMM toolbox for computational protein design. Syst Synth Biol 2, 105–113 (2008) . Download: PROTDES.tar.gz

AutoBioCAD: Computational design (fully automated) of regulatory circuits in E. coli able to provide the nucleotide sequence (maybe the only available software that is fully unsupervised with this capability). Please cite  Rodrigo, G. & Jaramillo, A. AutoBioCAD: full biodesign automation of genetic circuits. ACS Synth. Biol. 2, 230–236 (2013). Download (this software replaces the obsolete Genetdes): AutoBioCAD for MacOSX (version 10.5.x), AutoBioCAD source code without libs (tested in SuSE 11 Linux), AutoBioCAD source code with libs (tested in SuSE 11 Linux)

Desharky: Computational design (fully automated) of metabolic pathways in E. coli. Please cite G. Rodrigo, J. Carrera, K.J. Prather, and A. Jaramillo. DESHARKY: Automatic design of metabolic pathways for optimal cell growth. Bioinformatics 2008 24(21):2554-2556. DOI:10.1093/bioinformatics/btn471). Download:

RiboMaker: RNA server for the computational design (fully automated) of riboregulators: RiboMaker