How optimize the Size Exclusion Chromatography?

Hello! I'll do a size exclusion chromatography, but I only have an open column, and I'll perform the peptide extraction from yeast, using buffer lysis (sodium phosphate 50 mM/NaCl 30 mM/DNAse and...

01 March 2021 2,215 2 View

How to make Fast Green FCF from powder?

Hi everyone We need Fast Green to electroporate plasmid into mice embryos, therefore we simply need it to see some color in the liquid we are electroporating so that electroporation is more...

07 February 2021 1,671 2 View

LINCS warning only with -pme gpu?

Dear all, I recently bought a RTX3080 and was unable to start the NPT and production steps due to lincs warning (my old gtx 1080ti card ran normally, using the same .mpd), I tried several...

18 December 2020 3,333 2 View

What is the relationship between induction machine stator reactance variation and slip?

It is possible to notice, at some three phase induction machine datasheets, that exists a relationship between stator leakeage reactance and slip, that is, the stator leakage reactance increases...

23 November 2020 2,949 3 View

How to characterize the pore size of membrane filtration with bubble point method?

Hello everyone, I am having troubles with the bubble point measurement to find the pore size of my self-fabricated microfiltration membrane, and I couldn't find a proper answer anywhere else. It...

16 November 2020 7,574 1 View

Is there same kind of limit when annealing two DNA products?

Hi there I'm planning on annealing two PCR products to perform some mutagenesis in a plasmid. I was recommended to try and keep it to 600pb each, for example, but for one of the plasmids there...

15 November 2020 8,656 3 View

Is there any way to learn a neural network based on a cost function that makes use of a root finding algorithm?

I need to integrate a root finding algorithm in a neural network. For that, and in order to be able to perform backpropgation I need the algortihm to be differentiable. Is there any method/...

05 November 2020 1,361 3 View

LiFePO4 DRX peaks?

05 October 2020 8,919 3 View

What software (preferably free) is most recommended for solving Mixed Integer Linear Programming (MILP)?

I need to model a construction and demolition waste management network in order to maximize waste recycling. I read some works that use MILP. Among the software used are GAMS, JULIA, MATLAB and R....

27 September 2020 9,230 9 View

What are the effects of phosphorus deficiency on dehydrogenase activity in soil bacteria and fungi?

I suspect that under phosphorus deficiency the electron transport chain in the plasmamembrane and mitochondria of soil bacteria and AM fungi, respectively, is disrupted as a result of lower ATP...

30 August 2020 4,659 3 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