Is it possible to superimpose different ligands in swiss dock

11 August 2017 1 9K Report

i am using swiss dock for my compuonds. Is it possible to superimpose different ligands and standard molecule at the active site in swiss dock

Mohammad Tarek

unfortunately, the server rejects multiple ligands in a file

Badges
Science method

Similar topics
Biological Science
Ecology

More Shaheen Begum's questions See All

What is the average stove efficiency for household gas stove especially in the Indian subcontinent?

In one paper, I saw it to be about 36%. But as the paper was published in 1997, shouldn't modern household gas stoves be more efficient?

14 December 2020 6,199 6 View

Is there a guide for Aspen Hysys to show unit operation calculations?

For example, let's say if I design a conversion reactor and give inlet temperature,pressure,composition and reaction kinetics then Hysys will show me the outlet conditions. It doesn't,however,show...

09 December 2020 8,375 3 View

Mymensing med J 2014 Oct;23(4):770-773. I am one of the co-author but research gate showing different name. What is the solution?

I have already mentioned that i am one of the author of Mymensing med J 2014 Oct;23(4):770-773. Article titled "Association of infertile patients having polycystic ovarian syndrome with recurrent...

04 October 2020 2,148 1 View

Which decision rule algorithm is best in machine learning? Is there any algorithm based on rough sets that gives good results?

I am trying to learn some algorithms that extract decision rules from data sets, particularly by using rough sets. I need to know whether they are reliable and efficient (like LEM2) for real datasets?

17 August 2020 7,013 6 View

Do you think to present the article in a conference to waste the money only?

At present there are huge fund needed to attend in a conference for.presenting research work. Unfortunately, I faced that there are no good feedback or concrete ideas to develop the writings of...

26 March 2020 2,062 10 View

Glycan analysis by capillary electrophoresis (CE-LIF) ?

Hi, We want to perform glycan analysis using tissue samples (human and mouse). We consider to purchase a capillary electrophoresis machine P/ACE MDQ, however we are not sure if it is user...

14 November 2019 4,911 3 View

How can a penal primary data be run into SPSS?

12 November 2019 4,810 2 View

Does surface particle size (surface component) has any relation with atmospheric optical depth (atmospheric component)?

I have estimated thermal inertia for a surface followed by its particle size, I have to look for the relation between particle size and atmospheric optical depth, I have gone through the...

11 October 2019 7,986 3 View

Techniques which can be used for delineating the rim of a feature?

Hi, I want to delineate the rim of this crater (refer attached image) using remote sensing software, apart from visual interpretation what are the other available techniques which i can opt...

06 September 2019 9,987 3 View

Is there any data set from where i can find country wise data on FDI & portfolio investment inflows in Pakistan?

i need data on private capital inflows in Pakistan, for this sake i have to generate the variable by adding FDI in the reporting economy and the private elements of portfolio investment, financial...

07 July 2019 4,316 5 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