Has someone already used deprotonated (charged) ligands for the AutoDock molecular docking?

More Sergey Shityakov's questions See All

How do we pick data for determination of Validation Acceptance Criteria?

Hello, colleagues! There is commenting open for new upcoming edition of USP 1033. Validation target acceptance criteria is now different from what it used to be and it doesn't include Cpm....

23 July 2024 7,292 3 View

Hydride zirconium properties?

Could you present the review or nowadays status state investigation of thermophysical and physico-mechanical properties of hydride zirconium (ZrH2)? Where can I find out properties data tables?

02 April 2024 2,025 0 View

Ansys APDL_Receiving resulting heat flow in finite element?

Could anyone explain *how to* or give an example of receiving heat flow (watt) for the FE element? I understand that *GET command is useful like *GET, PAR, ELEM,NO_ELEM,...,SMICS but can't get...

01 April 2024 6,562 2 View

Is it possible an unspecific binding of streptavidine or peroxidase?

I have a question for the professionals. The essence of the problem: I fix the oligos on a plastic substrate, they play role of primers in solid-phase PCR. I carry out a one-step PCR with...

28 March 2024 9,110 2 View

Simulation of temperature field in a brick, taking into account thermal expansion with ANSYS Mechanical APDL? (Thermomechanics in details)?

Problem to model a simple (at first glance) stationary problem of thermomechanics in an elastic formulation in ANSYS Mechanical APDL. There is a simple block (brick), with spatial non-uniform...

28 March 2024 7,709 2 View

Ansys Mechanical APDL__4D table input (axes and indices)?

Hello colleagues! Several days ago I used to struggle with tech problem of 4d table input QV = QV(X,Y,Z,TIME) using Mechanical APDL commands script. I haven't solved it yet. 1) Standard technique...

22 March 2024 3,515 0 View

I am looking for B-H curves of GO steel M080-23DR (Domain Refined)?

I am looking for B-H curves of GO steel M080-23DR (Domain Refined). It is customary to think that the "technical saturation" of GO steels is near 2.0 – 2.04 T. However, there are some indications...

04 March 2024 7,393 0 View

How to get solution for house-selling task (or task of selling an asset) with conditions “finite horizon, recall is allowed” ?

House-selling is one of the typical tasks of the Optimal Stopping problems. Offers come in daily for an asset, such as a house, that you wish to sell. Let Xi denote the amount of the offer...

03 February 2024 4,482 4 View

What dye do you use for RNA electrophoresis?

Colleagues, tell me which dye is optimal for staining RNA during gel electrophoresis? Which one do you use in your laboratory?

21 January 2024 6,373 4 View

Are you in Public Health and interested the project: "Central Asia Alliance for Climate-Health Research"?

I seek coauthors and colleagues from Uzbekistan, Kazakstan, or other CA countries in "climate-air-pollutant-health" research. It would be great to collaborate with individuals who share similar...

28 November 2023 8,493 0 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

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

Why aren't most metal oxides insoluble in water?

Why BaO (s) + H2O(l) ---> Ba 2+(aq) + 2 OH - (aq) if Oxygen loves owning all the electrons, why would it bind to hydrogen which competes with Oxygen for electron ownership more so than...

03 August 2024 5,392 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

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

How to add Cr parameter in autodock?

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!

29 July 2024 488 0 View

Sanket Bapat

AutoDock has limitations at many levels, in such cases MOE or GLIDE docking tool gives much better results.

Euzébio Guimaraes Barbosa

If you are not interested in the scoring but binding pose you may dock a valid as close as possible structure. Modify it to what you really want using other software.