30 Questions 104 Answers 0 Followers
Questions related from Joel Subach
Hi RG, towards the above topic, my understanding is that a dual drug´s target towards binding is: 1. binding two separated oligomers 2. binding one oligomer exhibiting two targets within one...
24 November 2024 8,540 0 View
Hello RG Forum, towards the above topic, I am running the Orca Command: (base) Joels-MacBook-Air:14C-DON-C8i joelsubach$ orca 14C-DON-C8i.inp > 14C-DON-C8i.output.out (in this case DON means...
05 November 2024 4,450 1 View
Hello RG Community I hope your well:), towards the above topic, I have generated 10 ligand 3-D Conformational Structures via a SMILES within PubChem, there are no PDB Images yet for this...
11 September 2024 2,039 1 View
Hello RG Community, I hope you're well:). Towards the above-topic, my Acceptor Ligand C5 ffTK Water Int Tab generated .inp File exhibits water coordinates that need to be flipped to the other side...
12 July 2024 8,366 0 View
Hi RG Community I had input all the appropriate files, however, received an Action halted on error! My ORCA generated .gbw QM Output file was not recognized (please see screenshot attached). I...
16 February 2024 2,592 1 View
Hello RG Community:), towards the above topic: I had entered all of the appropriate files within the ffTK Opt. Charge Tab, however, am generating the below errors upon Run Optimization (just the...
29 January 2024 8,598 2 View
Hello RG Community:), I have a ligand exhibiting penalties between 10-50 within a .str file generated via a CGenFF, the generated .prm file does not exactly match the ligand atoms nor the closest...
26 December 2023 4,414 1 View
Hi I had modelled a heptamer transmembrane protein missing 10-residues within the extracellular loops via MODELLER constraining the known residues as a heptamer (when MODELLER modeled as a monomer...
09 December 2023 4,552 0 View
Hello towards the above topic, I successfully loop-modeled a transmembrane heptamer protein (426-residues per monomer) exhibiting 7-extracellular loops each missing 11-residues via MODELLER via...
04 December 2023 9,576 2 View
Hello RG Community I hope you're well:). For the above topic I only need to optimize two-dihedral angles, can I therefore only select Scan and Opt Torsion tabs and ignore the others i.e. Opt...
18 October 2023 7,513 1 View
Hello RG, I input my generated ORCA output.out files into the ffTK Opt Torsions Tab and then Ran Optimization and have instead generated: No provisioning arguments specified Warning: Ignored...
17 October 2023 6,383 1 View
Hello I am receiving the error: 'utf-8' codec can't decode byte 0xa9 in position 11: invalid start byte when I visualize my HETATM PDB File via Pymol that I extracted from my docked...
04 January 2023 8,638 3 View
Hello, for the above topic I understand there maybe other variables, however, in general? Thanks:)
08 December 2022 3,780 0 View
Hello, I am having a little trouble with properly formatting a ligand file where Pymol is exhibiting the following error (see screenshot) for the attached pdb file. If this is something that you...
02 December 2022 9,815 3 View
Hello for the above topic, I believe that the membrane would influence the docking and accordingly be executed subsequent to protein-membrane implantation, opinions? Thanks:) Joel 🚀
21 November 2022 4,234 0 View
Hello:) for the above topic I have cut and pasted an A-chain from a heptamer but can not Pymol visualize this A-Chain nor model this, how would this technique be properly cut (what needs to be...
28 August 2022 7,230 4 View
Hello I hope you are all doing well.:) Several transmembrane Pannexin1 3-D coordinate files have been submitted to the PDB, however, I believe all are missing coordinates in some of the Pannexin1...
12 August 2020 5,116 3 View
Hello, How Many Different Individual Postdoctoral Fellowships are there for a US Ph.D. (e.g. F32)? Success ratio(s), F32 applicants per year vs. #s awarded the F32 that year? Much Thanks:) Joel
24 February 2020 3,401 2 View
Hello is anybody savvy in this above topic? Kind Regards, Joel Subach Ph.D. Nanomedicine Rutgers
22 February 2020 4,157 0 View
Can in-silico designed nanoparticles be validated in-silico or only via a wet-lab approach? Thanks:)
02 September 2018 2,465 3 View
Hi, i have one unknown transmembrane protein that I am trying to make a pdb structural file out of. I ended up breaking it down into five-different model pdb coordinate files via Modeller via 5...
17 April 2018 5,890 7 View
Hi, which tagged nanoparticle 1-2nm in diameter is best for an in vivo delivery towards Macrophage and CD4+ T cell-protein-membrane attachments? Meaning which nanoparticle is most biocompatible,...
10 November 2017 2,603 6 View
My understanding is: 1.) via HIV's high mutation rate creating very high antigenic variability (no reply needed for 1.)) 2.) via its antigenic inability to provoke and immune response, a.) why can...
03 October 2017 7,160 12 View
Hello, During conventional virus assay what percentage (%) of detected proteins are from complete virions vs. just protein fragments detected? For example the VP proteins of Ebola are inside of...
05 April 2017 3,472 0 View
Which is the most conserved and unobstructed epitope of Ebola Virus?
30 March 2017 3,886 12 View
How did Einstein's Spacetime pull of gravity on the Planet Mercury differ in value than Newtons? Was it simply via the spacetime fabric adjusting this value? Thanks:)
07 February 2017 8,696 51 View
Hello, when a patient is first infected with Ebola my understanding is that there is not really a primary viremia and for the first week Ebola just sits in the organs and or white blood cells...
08 December 2016 4,752 7 View
Does Ebola leave a specific antigen upon infected cell membranes? If yes which antigen?
28 July 2016 8,414 2 View
Hello, do any experts on Ebola know the Ebola serum concentration at diagnosis time? Thanks:) Joel
27 July 2016 3,387 34 View
During a viral diagnosis for a complete virus particle, its antigen, or its nucleic acid, what portion of the patient sample being detected is the complete virus vs. pieces of its antigens or...
22 July 2016 6,670 2 View
