Can I dock a protein and a diadenosine polyphosphate nucleotide(protein's ligand)? If yes, then how?

More Riya Sethi's questions See All

In PRIMER, is it possible to downweight certain taxa in multivariate community datasets to reflect uncertainty around identification??

I have a dataset with about 80 different species. As usual, some species are very easy to identify with certainty whereas others are more difficult, which means that I am less certain of my...

03 March 2021 8,066 4 View

How to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

How to grow E.coli on the low salt LB agar plate with 50 or 100ug/ml of Blasticidin?

Hello, I would like to ask how to grow E.coli which resists 50 or 100ug/ml of Blasticidin. I have tried many methods by using low salt Luria-Bertain(LB) agar plate. However, no colonies grow. Let...

01 March 2021 2,027 2 View

OpenBCI eeg--has anyone used them?

I'm looking to try out an off-the-shelf EEG set for some exploratory work. Curious if anyone has used the OpenBCI, and how much set-up work is required. I've heard they are more difficult to get...

01 March 2021 4,128 3 View

How to remove DCU and HOBT from my reaction?

I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??

28 February 2021 2,153 1 View

1 nm thick MgO thin-film to be deposited on Si wafer using thermal evaporation. What will be the optimum deposition conditions?

Favourable conditions of base pressure, rate of deposition. Also, by which characterisation technique to be used to verify the thickness of the deposited film.

28 February 2021 3,640 3 View

How to eliminate Steady state error from Reinforcement learning genetic algorithm code?

The following code (see 1st 2 images attached) is used to produce PID controller values that are designed to control the system (G). The code finds the PID controller values (noted as k) by using...

28 February 2021 6,560 14 View

B-mercaptoethanol (BME) protocol?

Hi everybody, I have been running a multiplex IHC which allow me to stain the same tissue with different markers (Primary Ab + Secondary conjugated Ab) (AF487, AF555, AF647). Since I would like to...

27 February 2021 5,028 2 View

What is the suitable range of Sulfur content and Viscosity of Heavy fluid Oil that used in Kiln?

What is the disadvantages of high sulfur content to the ceramic burning process? and what is the effect of outranged viscosity?

24 February 2021 8,219 2 View

Anybody with an idea on how do design specific primers for detecting tomato resistance genes tm-1, TM-2 and Tm2^2?

I am trying to identify these 3 genes among some tomato cultivar collections and after aligning some sequences from NCBI, I couldn't find unique sequences to target for specific primers. There...

28 February 2021 606 3 View

RIA. How to measure?

When you use RIA, with a control the unknown sample with antibodies, you bare in mind the binding sites of the antibodies. However you still need to measure labelled antigen (radioactive) and not...

28 February 2021 2,133 3 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

What is the best temperature to coat an ELISA plate?

Hello, I want to control the temperature of my ELISA plate during incubations to get consistent results. In general, what is the best temperature to coat the plate with antibody? I have been...

16 February 2021 2,377 7 View

Can Immunogenic BNT162b vaccines protect HUMANS from SARS-CoV-2?

"A safe and effective vaccine against COVID-19 is urgently needed in quantities sufficient to immunise large populations. We report the preclinical development of two BNT162b vaccine candidates,...

11 February 2021 6,628 9 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 nr blast important?

Hello, I have designed a specific primer for my Gene, when I blast this primer, it just finds the mRNA of the gene, but in nr blast, I have found some CDSs that are not relevant to my Gene. Do...

05 February 2021 5,842 3 View

Multiple insertions with Q5 Site-directed mutagenesis?

03 February 2021 221 2 View

Difference between assessing EC50 in presence of physiological levels of human serum albumin and alpha1 acid glycoprotein vs. % human serum?

01 February 2021 1,825 1 View

How would you assess protein binding adjusted EC50 for a drug that has a binding rate of over 95%?

I'm in need of a reference or a method to come up with a protocol that allows one to get the protein-adjusted EC50 for an antiviral drug in presence of human serum albumin and acid glycoprotein.

27 January 2021 1,402 1 View

Vasavi Malkhed

haddock server you can use

Riya Sethi

Vasavi Malkhed Can I also identify the amino acids residues at the active site?

Sargol Mazraedoost

AutoDock:AutoDock is a widely used molecular docking software that can perform protein-ligand docking simulations. It allows you to predict the binding conformations and binding energies of ligands to your protein.

AutoDock Vina:AutoDock Vina is an improved version of AutoDock, offering faster and more accurate molecular docking. It is user-friendly and allows you to perform high-throughput virtual screening.

DOCK:DOCK (A Program for Biomolecular Cavity Detection) is a versatile molecular docking program. It can be used for both protein-ligand and protein-protein interactions.

UCSF Chimera:While primarily a molecular visualization tool, UCSF Chimera can perform molecular docking using the "Dock Prep" and "DOCK" functions. It is known for its user-friendly interface.

Schrodinger Suite (Glide):The Schrodinger Suite includes the Glide module for molecular docking. It's widely used in pharmaceutical research for virtual screening and protein-ligand interactions.

PyRx:PyRx is an open-source virtual screening software that integrates with AutoDock, AutoDock Vina, and other tools. It provides a graphical interface for docking simulations.

MGLTools:MGLTools includes a suite of tools for molecular modeling and docking, including AutoDock and AutoDock Vina.

Computational Methods:

Binding Site Prediction: Use bioinformatics tools such as CASTp, SiteMap, or Fpocket to predict potential binding sites on your protein's 3D structure. These tools analyze the protein's surface properties and identify cavities or pockets that are likely to be binding sites.

Docking Studies: Perform molecular docking studies with known ligands or substrates to predict the binding site location. Analyze the binding poses of ligands within the protein's structure to identify interacting residues.

Binding Site Residue Analysis: Use visualization software like PyMOL or Chimera to analyze interactions between ligands and amino acid residues in the predicted binding site. Look for hydrogen bonds, hydrophobic interactions, salt bridges, and other binding interactions.

Sequence Analysis: Use sequence-based methods to identify conserved residues within the protein family that may be part of the active site. Multiple sequence alignment and conservation analysis can provide insights into functionally important residues.

Structure-Activity Relationship (SAR) Analysis: If you have experimental data on ligand binding and activity, perform SAR analysis to identify residues critical for ligand binding and biological activity.