Is it possible to perform docking of Protein having Mn or Mg ion by AutoDock Vina?

More Vinod Kumar Gurjar's questions See All

Can ImageJ software be used to quantify collagen from Masson's-Trichrome stained images?

I am after quantifying the blue stained collagen in a Masson's-Trichrome stained skin section from an immune deficient mice and compared the same with its WT control. I am curious to know can...

17 February 2021 384 3 View

Which software is best for geochemical data analysis and graphics for Geochemical Modelling of Igneous Processes?

I'm familiar with Geochemical data analysis software such as GCDKit, PetroGraph, and Petroplot etc. which one is best and suitable for doing Geochemical Modelling of Igneous Processes? I need...

22 December 2020 9,300 2 View

How to make a high spatial resolution land use land cover map in a 10 year temporal resolution with respect to Indian scenario?

I want to create a large scale land use land cover change map of a village of India in the 10-year interval. Which one is the appropriate satellite image for this. and anybody kindly explains the...

12 October 2020 3,996 6 View

How to calculate new human dose based on In-vivo animal study results?

I have performed In-vivo study in rate model for new formulation as well as marketed formulation. Based on results new formulation have significant improvement in all PK parameters. Oral dose...

20 August 2020 2,209 1 View

Please suggest journals (SCI or SCOPUS) for publishing a review article of Microwave/ Antenna field ?

Please Suggest journals for publishing review articles related to antenna field

18 May 2020 8,119 23 View

What are the fluorescence based experiments to determine interaction of receptor?

i want information on fluorescence based experiments

17 February 2020 1,805 1 View

What can be the measurement scale for perceived employee performance management?

I am doing a research in Cement Industry with emphasis on perceived employee performance management. I am looking for the measuring scale of the same.

09 January 2020 6,363 3 View

How can we extract lactic acid from the biocrude derived from the hydrothermal liquefaction of biomass?

I am trying to separate lactic acid via distillation, from the bio-crude I got after performing hydro-thermal liquefaction of biomass. however, it seemed very challenging as always other organic...

07 January 2020 9,265 1 View

How can I confirm protein expression from Pichia pastoris colonies?

I was successful with the transformation( pPIC9K vector in Pichia pastoris GS115 strain )and got good colonies in RDB plates after 48 hours. later in MD and MM plates also. Can anyone please tell...

09 December 2019 6,346 8 View

Why only Sulpfacetamide is most suitable drug for eye drop preparation not other sulfa drug?

i want to prepare some sulfa drugs ophthalmic formulation

05 December 2019 8,017 2 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

How to model Supercritical water gasification (SCWG) process in Homer software?

Hi everyone How to model Supercritical water gasification (SCWG) process in Homer software?

25 February 2021 4,075 1 View

What program can I use to caclulate dipole moment efficiently and without the need of excessive computation?

Hi, I am a third year chemistry undergrad doing my group project in which I need to predict the HPLC retention time of 20 aromatic molecules. to do this we require the chemical properties of these...

24 February 2021 1,384 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

Any suggestions or recommendations on a good publishing house based on the African for academic books in the field of Communication and media studies?

I am currently working on a book on Public Relations (from an African perspective) and the rationale behind the book is the fact that as instructors in this field, we borrow instances and case...

19 February 2021 2,482 2 View

When to use different framework?

Hi, can I use both conceptual framework and theoretical framework in my systematic review? My future study plan is to use a theory. In this situation for my systematic review should I use both or...

18 February 2021 9,581 2 View

Person-Codes for questionnaires in longitudinal studies: Is there an easy solution for better matching-rates?

Hi, I have a problem regarding matching of longitudinal data in my field of research (university students). We have a Person-Code for matching data measured in different time points, but 30%+ of...

17 February 2021 3,075 4 View

Can anyone provide an advice on running a validation study of a commercially available product in collaboration with the manufacturer?

We are planning to run a study validating a commercially available product (i.e. software) and while we initially planned to do it independently of the manufacturer, they heard about our intention...

17 February 2021 2,295 3 View

What are the latest topics in strategic management area, esp those related to Quantum managment?

I am trying to involve science , in particular Physics, into Strategic Management studies for my master thesis . There are a number of papers discussing this topic but in such a fast changing...

13 February 2021 891 5 View

Yoshinobu Ishikawa

Hi Vinod,

Vina can do it, but is not good at handling Metalloproteins.

I recommend AutoDock 4 and/or idock for metalloproteins.

http://autodock.scripps.edu/

https://github.com/HongjianLi/idock

Martiniano Bello

Even autodock doesn't deal well with metals. I recommend better MOE or Glide.

Anu Manhas

Please find the attached article

Article Comparative Assessment of Seven Docking Programs on a Non-Re...

Anwesh Pandey

yes, you can add parameters for selected metals and then continue with docking.