A tool for finding TFs binding sites?

More Oskar Ciesielski's questions See All

Can I perform CellRox assay for Caco-2 cells treated with fruit extracts?

Hi, I am planning to check effect of fruit extracts on Caco-2 cells and DNA oxidation in them. As a oxidizing agent I planned to use H2O2. Has somebody used this test for cells interacting with...

28 January 2022 3,622 0 View

Free alternatives to QIAGEN Ingenuity Pathway Analysis?

Hello, Im looking for good free alternatives to QIAGEN's IPA, could you suggest some similar software? I'd preferably use a standalone version, not an online-based tool, it would also be great if...

03 January 2022 6,760 5 View

Final reasoning (Münchhausen trilemma): A new solution with layer logic?

Hello, when looking for (ultimate) justifications / final reasons, one comes across the Münchhausen trilemma: 1) One can always ask for a new reason for what has just been founded - So ends up...

21 April 2021 1,090 0 View

What are the major barriers in renewables adoption in Finland?

Barriers of different kind: regulatory, technological, socio-economic or market-related? What are the best methods/tools to overcome them? Please share your thoughts

25 March 2021 5,887 2 View

Interaction - a new non-local dimension?

Hello, in my research to a new logic I also encountered the following more physical problem: According to my theory it could be that the interaction of two particles was different (or not...

15 May 2020 6,329 2 View

Low temperature and bones ?

At what low (minus-below zero) temperature do human bones disintegrate - for example skull bones broke ? And how long they must be exposed on that ?

07 November 2018 6,886 11 View

What do you think about Polycaprolactone as a biomaterial ?

What do you think about Polycaprolactone as a biomaterial ? is possible made the glue for the dental prothetics on his basis ? Polycaprolactone is biologicaly neutral and resorbable so maybe it's...

23 May 2016 5,710 2 View

Is there someone who can say something about this morphological change in os malleus or met something similar ?

Broken anterior processus in one os malleus is almost the same size as manubrium. Is anyone met similar change ? Maybe it's normal variability ?Pictures and above question from my collegue /...

25 October 2015 7,162 17 View

Does anyone know the good source of lectures (with presentation) on the human population ecology ?

Can anyone share or indicate the source for lectures with presentations (ppt or other formats) on the Human Population Ecology ? With respecting copyright of course. I would be grateful for any...

11 October 2015 1,308 7 View

Does TE buffer lyse human white blood cells?

In an experiment, I prepared serial dilutions from fresh human blood samples (EDTA tubes) using TE buffer. Now I need to know if the white blood cells were intact or not in the diluted blood...

12 December 2013 9,937 6 View

Is artifacts in XPS possible to build high deviation in binding energy larger than 5 eV??

Hello. Thanks for your consideration to see my question. Recently, I conducted XPS anaylsis of g-CN that is prepared from thermal polycondensation of DCDA, so-called conventional bulk-g-CN,...

30 July 2024 9,824 2 View

Why binding energy is in positive number after performing mmpbsa?

I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...

19 July 2024 4,120 5 View

How to extract binding energy from pv.maegz file without using Schrodinger?

I have conducted virtual screening using Schrödinger on a database of 17,000 molecules. Unfortunately, I cannot use the system with the Schrödinger license at the moment. I am trying to find a way...

18 July 2024 2,881 4 View

Less substrate signals towards the last lanes of the Native PAGE?

I have been running native page for FAM DNA substrate ( fluorescence samples) for protein DNA binding reaction. Binding is there but towards the end of the lane , I am loosing signals...

17 July 2024 6,213 4 View

Anybody can assist me in Protein and magnetic beads seperation?

Hi, I hope you are doing well, I am working to remove DNA from protein sample by using silica hydroxode magnetic beads. I used different binding buffers but I din't get my protein band in initial...

02 July 2024 5,502 4 View

HADDOCK score and binding affinity, any relation?

I am working on Protein-DNA/RNA docking and using HADDOCK 2.4 server, but I couldn't understand the relation between HADDOCK score and binding enthalpy (if there is any). I want to find the...

09 June 2024 3,939 4 View

How to derive the tight-binding Hamiltonian by placing atomic orbitals at Wyckoff positions ????

Dear all, I am new to theoretical physics of condensed matter physics. I am trying to write down a hamiltonian to fitting my first principle calculation. I am confused how to get the hamiltonian...

05 June 2024 9,668 0 View

Does higher oxidation state of an element always correspond to peaks with higher binding energy in XPS?

For example, Mn+2 has a lower binding energy peak in XPS compared to Mn+3. However, Ru+3 has a higher binding energy peak in XPS than Ru+4. So what is the general rule that dictates which (higher...

02 June 2024 5,407 1 View

Is it possible that the binding energy of heavy quarkonia becomes more and more negative as the temperature increases?

I saw in many articles that quarkonia has negative binding energy and at some places it also has positive value but the pattern of binding energy is always decreasing...... Can anyone explain this...

15 May 2024 6,918 0 View

How can I determine the width and length of graphene nanoribbons using tight-binding or DFT models?

For easily able to understand I uploaded a image.

15 May 2024 9,768 2 View

Md Habibur Rahman

Dear Oskar

You can see the link https://www.networkanalyst.ca/

Julio Vera

Hi Oskar,

There are commercial tools like TRANSFAC, but also open-access databases.

See for example GTRD:

Article GTRD: A database of transcription factor binding sites ident...

Tommaso Mazza

JASPAR, of course, at https://jaspar.genereg.net/

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles Nucleic Acids Res. 2022 Jan 7;50(D1):D165-D173

https://academic.oup.com/nar/article/50/D1/D165/6446529