Can I use CB Dock as a tool of molecular blind docking for my publication? Is it reliable, if not what are some web based docking tools ?

More Sheikh Sunzid Ahmed's questions See All

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !

02 March 2021 5,785 3 View

What is the characteristic length to determine the Reynolds number for the scattered turbulent fluid flow?

Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...

02 March 2021 1,999 5 View

I am interested in medicinal chemistry field, which books are highly recommended to learn from?

I am at the beginner level in drug design and drug discovery, and I am interested to learn more about this field. Which books are highly recommended to start from and gives me all essential...

02 March 2021 8,437 2 View

Could you please recommend some good journal that accept very long revie papers (approximately 6000+ words) in neurosurgery, cancer biology ?

01 March 2021 8,087 3 View

Does anyone have kinetic and kinematic dataset for gait classification?

I want to differentiate between normal and abnormal movement. For this reason, I am looking forward to this type of dataset.

01 March 2021 9,485 1 View

How to assign different material properties to each element in Abaqus ?

Hello, I am writing a python script to generate my model and write the input file. The problem is I have 1000 elements in my mesh and I want to assign different material properties to each...

01 March 2021 9,511 3 View

How to choose ANN number of hidden layers and nodes?

Hello, Could you please share any interesting research explaining how to choose the number of hidden layers and nodes per layer in case of regression problems using ANN? Thank you, any help would...

01 March 2021 6,200 3 View

What is the best way to calculate the angles of twist for concrete columns subjected to torsional moment using finite element software?

In Finite element software like ANSYS , there is difficulty in obtaining direct results of twisting of concrete members because SOLID65 which is the unique element designed to represent concrete...

26 February 2021 3,806 2 View

How to identify what type of fillers are in a polymer?

Hello everyone, I have some PHAs blended with fillers and nucleating agents, yet I don't know what kind of fillers or nucleating agents. The producer has shut down and there's no way to get in...

24 February 2021 1,356 8 View

Can't recognize exact phase and PDF card no of Silicon carbide in XRD?

We have deposited silicon carbide on carbon substrate using one PVD technique. Due to amorphous behavior of SiC at low deposition temperature, we performed heat treatment of those films at...

22 February 2021 2,072 3 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

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 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

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

How to generate .dlg files on PyRx?

Hi. I'm using the PyRx version 0.8 and getting the error message: WARNING: Filename mismatch: "2DFN_ADP_CL.maps.fld" :: "..\2DFN_ADP_CL.maps.fld" C:\Program Files (x86)\The Scripps Research...

17 January 2021 843 3 View

Servers for finding free energy and dissociation constant of protein-protein docked complex?

Hello everyone, I would like to get help about finding any server or application which can give me info about free energy and dissociation constant of protein-protein docking outputs. I have...

15 January 2021 587 3 View

What would be the best option to dock a number of peptides to a protein?

I have been using PyRx to dock peptides to a protein. Initially the numbers were small so it was okay. But now I have to dock over 500 peptides and doing so manually would take forever. My...

10 January 2021 3,330 4 View

Is there any online webserver for DNA-ligand docking?

I have used Autodock 4.2 for docking studies and trying haddock for DNA-Ligand docking. It shows an error and not supported DNA PDB file. Suggest a template for DNA and ligand PDB file and also...

29 December 2020 1,322 8 View

I am looking to learn docking studies online can any one help?

I am interested in docking studies and want to work in that field looking for someone who can help and will guide.

22 December 2020 1,575 2 View

Edward Ntim Gasu

Check if PyMol or BIOAVIA Discovery Studio can view. Else, change the .crd to .pdb to view in UCSF Chimera. You can attach the said file, in a comment, if all trials fail, I can try to convert for you…

Sheikh Sunzid Ahmed

Thanks Edward for your kind help.

Ricardo J Ferreira

Hi,

the best software for blind docking is qvina-w.