Which tools are best for prediction of binding pocket or active site of protein to perform molecular docking?

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Unexpected 35 kDa Band Observed During Expression and Purification of Dengue 3 NS5 RdRp Domain ?

Background: I am developing an RdRp assay for Dengue virus-3 and need to express and isolate the NS5 protein's RdRp domain (~101 kDa). My expression vector includes a GST tag followed by a 6x His...

13 July 2024 9,950 3 View

How is artificial intelligence being utilized to enhance the diagnosis and treatment of sleep apnea?

AI has the potential to improve the management of sleep apnea by personalizing treatment, enhancing diagnostic accuracy, and advancing our understanding of the condition.

03 July 2024 9,393 2 View

How to dilute my DNA Template( 1 Micromolar stock solution ) into1 × 10-8 nM to 1 × 10-15 nM ?

How can i dilute my master stock of 1 micromolar DNA template to different concentration by serial dilution

17 May 2024 3,641 2 View

Why can't Ansys HFSS be used for LiDAR Based Simulation?

Hey All, I am currently trying to simulate an FMCW Lidar in Ansys HFSS which I used for RADAR Simulation and I cannot find a way out to perform Lidar based simulation. If anybody knows how to do...

20 March 2024 2,749 2 View

Hi, A phospholipid qualitative analysis is to be performed in liposomal formultations.Is HPLS-UV a reliable technique for same ?

A phospholipid content has to be estimated in liposomal formulations.Is HPLC-UV a reliable technique for same or should other techniques be employed?Which one is the most suitable of them all ?

22 November 2023 4,883 1 View

How to generate ligand.itp and ligand.gro files for md simulation using amber14 force field?

How to generate ligand.itp and ligand.gro files for md simulation using amber14 force field?? Kindly help!! Thanks in advance.

12 November 2023 2,434 4 View

Where I can do extrusion of Magnesium alloy in india?

Any vendor or Institute.

05 November 2023 3,030 0 View

Error while generating ligand topology?

I'm trying to generate ligand topology files through CHARMM FF but i'm getting this error. I installed the respective python version but error is still same python cgenff_charmm2gmx.py UNK...

23 October 2023 1,587 4 View

How can I insert a protein structure model within Lipid bilayer structure model?

How can I insert a protein structure model within the Lipid bilayer structure model? Kindly help.

12 May 2023 5,082 3 View

What are the alternate servers for PRODRG to generate ligand topology? I have tried ATB, ACPYPE also but ligand gets detached from the protein?

what are the alternate servers for PRODRG to generate ligand topology? I have tried ATB, ACPYPE also but ligand gets detached from the protein while generation complex.gro file in the MD run....

23 April 2023 7,765 3 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,988 3 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 1,494 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 7,726 4 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 to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

Is it possible to dock more than one drug in the same active site or pocket of a protein to study synergistic/antagonistic/additive properties?

I wanted to know whether we can observe the synergistic/antagonistic/additive properties of combinations or mixtures of compounds through docking analysis. But during docking preparation any...

28 July 2024 7,413 6 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View