I have docked 2 ligand simultaneously and tried to get 2d interactions with ligplot+ but in ligplot+ it is showing only one ligand ?

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How to find the mean, SD and CI in SPSS?

Hi, I hope that someone can help me with this task: I have 5 groups of participants which are numbered in SPSS from 1 to 5 (according to their group number) and are all under the variable group....

03 March 2021 506 3 View

Do you know any MR image dataset?

I would like to research on MR images (0.5T and 3T). Can you please suggest some websites that I can download dataset including both 0.5T and 3T MR images? Thank you.

02 March 2021 7,735 3 View

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

28 February 2021 3,864 3 View

What pH condition required to coat APTES on silica coated Fe3O4?

It's a hydrolysis reaction, which may produce by either acid or base-catalyzed reaction. so can anybody help me with this, which condition is suitable for this reaction?

26 February 2021 1,760 8 View

What software programs can directly simulate Additive Manufacturing Directed Energy Deposition (DED)?

I understand there are a lot of software programs that can simulate DED by going through specific modeling, simulation, and commands. For me, that was time consuming and results were not accurate....

24 February 2021 4,428 3 View

What condition required for coating of Fe3O4@SiO2 by using APTES?

I tried coating Fe3O4@ SiO2 by using APTES in 5% water-ethanol but it is not coated. Kindly suggest a solution for it. Thanks

24 February 2021 5,992 4 View

How can I prevent bubbles from forming under a coverslip?

My colleague and I are having some trouble mounting 70 micrometer mouse brain slices. When we initially position the coverslip over the mounted slices, there are no bubbles but when we come back...

10 February 2021 3,580 1 View

What recipe of homemade lenti-virus concentrator do you use?

My lab is using a lenti-X concentrator. And we are looking for a homemade recipe. I have tried this recipe....

08 February 2021 5,965 1 View

What is the best visualisation solvent for xylooligosaccharides using TLC?

I am interested in using TLC to detect non-linear xylooligosaccharides. What would be the best visualisation solvent? Would aniline phthalate solution be suitable? I have also seen people...

02 February 2021 7,748 3 View

Desalting using DSC- 18 SPE columns?

I am looking forward to remove excess of salt form my metal based porphyrin and trying DSC-18 columns for the same, can someone suggest me how how can one decide the polarity of the solvent to...

01 February 2021 9,076 1 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How long does it take to design and validate transition state analogue inhibitors?

Hi, I'm asking from the point of view of designing a research plan: How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope...

14 February 2021 2,610 1 View

How to check if the PMF profile obtained from ABF simulation is correct?

I am doing ABF simulations to calculate ligand binding enegy. The PMF profile that I get using single long ABF simulation is attached as pmf_total.png. When I do this ABF calculation with 10...

10 February 2021 4,170 2 View

Ligands with 3,4,5-trihydroxyphenyl group?

Hi In the design of a bidentate ligand with imine group, is it okay to have a 3,4,5-trihydroxyphenyl group in the structure? In other words, does the 3,4,5-trihydroxyphenyl group compete with...

08 February 2021 4,977 7 View

How to Remove different version of atom from pdb Crystal Structure for Docking Preparation?

I am new to Docking and MD, and currently try to catch on it. I try one of the webserver for docking, but unfortunately not working. it says " Your PDB contains multiple forms of the same residue...

08 February 2021 7,426 3 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 View

How do you get around this AutoDock Vina error?

I get the following error messages after running the simulation: Sorry, there are no Gasteiger parameters available for atom ligandx.ligand:A:lig1:O7 AutoDock Vina ligand docking initiated for...

26 January 2021 3,822 3 View

The dimensionality of protein and ligand is reduced after docking?

I used autodock to complete the docking between the ligand and the protein. I have a question, why the dimension of the result after docking is much smaller than the dimension of the protein...

24 January 2021 7,363 3 View

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

23 January 2021 3,975 7 View