Hi Joseph, ChimeraX does not itself predict protein structures, but it has simple peptide-building described near the bottom of this message, as well as interfaces to run other software: AlphaFold (actually ColabFold) - which runs on Google Colab, only short calculations are free, longer you may need buy a paid plan from Google <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> ESMFold <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> Modeller homology modeling (based on a similar structure), but commercial use requires getting a separate license for that <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> However, (1) it looks like this structure has a lot of disulfide bond crosslinks and our interfaces to other software would not handle that type of situation. PSA stands for several different things, if you mean prostate specific antigen, it does have several crosslinks in it, but that leads to #2 below: (2) If you search the Protein DataBank (PDB) of known structures, there are several structures for human PSA (e.g. https://www.rcsb.org/structure/2ZCH ). I don't know if they are the conformation (nicked form??) that you want. However, if you can find one that is the form you want, you can open that known structure in ChimeraX, use ChimeraX to create a peptide of the additional 7 amino acids, and then stick them together. It would not "predict" the real conformation, however, it would just be your own manual building. See Build Structure tool <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> ...in that tool, use the Start Structure section, choose "peptide" to build peptide <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start> ...in that tool, use the Join Models section to combine the peptide that you just built with the existing protein structure that you already opened in ChimeraX <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> ** Preferably somebody with a background in protein structure and molecular modeling would be tasked with this project. ChimeraX is just a tool, and depending on how it is used, you can do lots of modeling which may or may not make sense physically, and it is easy to do the latter. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2024, at 1:19 AM, Joseph Clifford via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I hope this email reaches you well.
I am a R&D scientist at Randox Laboratories and was wondering if possible could you model the nicked free form of PSA with the additional 7 amino acids at the N-term.
I am exploring the capabilities of chimerax and want to put a business case together to my manager regarding this software application.
<image.png> Many thanks in advance, Joseph Clifford