What is the cause of same results for all output ligands in surflex-dock?

More Afsane Heidari's questions See All

Deadly does of wood vinegar ?

How much is the deadly does & food toxicity of wood vinegar ?

25 December 2023 4,773 0 View

How can I pass field variable from USDFLD to FILM subroutine in ABAQUS?

I want to use field variable passed from USDFLD subroutine in a FILM subroutine in ABAQUS. Although FIELD(NFIELD) is one of variables which can be passed in for information in the FILM subroutine...

30 September 2023 9,662 0 View

Is wood vinegar potentially toxic to insects and bees?

03 September 2023 351 2 View

Would you please help me with my Prism file?

Dear colleagues I had a Prism file containing data until a few days ago; it opened without any problems Now it gives an error and does not open. Can anyone help me? Thank you

31 August 2023 8,817 1 View

How to fix the error of using IEEE style referencing in word by Mendeley's xml files?

As you now , Microsoft word just inserts .xml files as references' citation source. Mendeley exported xml files are readable in Microsoft Word but there is a problem: when i use IEEE style in word...

27 July 2023 7,312 4 View

What is the reason of vigor loss in F1 hybrids ?

Hello everyone as we know single crosses are known for highest heterosis in hybrid production method compared to their parents (inbred lines). but what has been happened to this F1 progeny (for...

12 June 2023 228 13 View

Dears , can anyone help me about lentivirus production with high weight transfer vector?

I produce lentivirus but the titer is very low, can anyone guide to me how to increase the titration and my transfer vector is high weight I think the low titer of the virus is due to the high...

30 March 2023 5,476 1 View

Dose anyone face this problem during corrosion test( jumping in current during corrosion test)?

while I am doing corrosion tests, a problem occurs. a jumping in current happens. dose anyone knows, it's a problem of my potentiostat or my electrodes? the image of corrosion test is attached....

29 January 2023 7,105 4 View

How is it possible to have in RIN results, extra peaks in addition to normal peaks for common RNA markers?

I performed RNA extraction and by Agilent machine I got the RNA quality check ( RINe). In result graph, I have more than 3 sharp peaks (5s, 18 and 28s rRNA peaks) and one more that I do not have...

04 January 2023 9,982 0 View

Can someone explain the following terms?

Can someone explain the following terms? ethanol (2X): what is alternative case it? PTFE membrane with a 0.45 micro meter pore size: what is alternative case it? polyester fiber (Carpenter Co.):...

24 December 2022 408 1 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View

How to improve plaques in Double Layer Agar Assay?

Hi all! My thesis groupmates and I are working on purifying an E. coli bacteriophage. The phage was handed down to us by the previous thesis group, but they only managed to purify it to about...

06 August 2024 5,801 4 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

Research Methodology - Impact of Corporate Reputation on Stakeholders Behaviors?

Please can anyone support with the survey questions based on RQ measures and propose how to do it in FMCG industry and include as well the role of brand equity Thanks

06 August 2024 949 0 View

Anyone having idea about VN primer for miRNA primer design ?

How to design VN primer to attach with universal reverse primer

05 August 2024 2,116 3 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Erma Fatiha Muhammad

Hi Afsane, did you optimize all the ligands before run into docking?

Vikash Kumar

First try to get the correct 3D conformation of ligands.

Mohamad Akbari

Hi Missis Heidari

Probably you set incorrect setting in Sybyl. I recommend you try again and review your setting with tutorial to find problem. but the first answer may be true however you can get different result .

Afsane Heidari

Thanks to all of you. I think finding my answer. I optimize ligands but I used .mol2 format. I did again using SLN format and my problem solved.

Did anybody applly surflex-dock using a format except SLN for ligands?