User: Tofayel Ahmed

gravatar for Tofayel Ahmed
Reputation:
40
Status:
New User
Location:
India
Last seen:
6 years, 11 months ago
Joined:
7 years, 12 months ago
Email:
s**************@yahoo.co.in

Project Associate, Dept. of Biotechnology, IIT Madras, India.

Posts by Tofayel Ahmed

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Converting Sdf Format To Pdb Format
... thanks a lot. I think u have generated this using Ligprep in maestro. However our institute haven't purchased maestro. though it will help me in having an idea about the 3D strc but still need to find out free tools for converting 2D to 3D. ...
written 7.7 years ago by Tofayel Ahmed40
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Comment: C: Converting Sdf Format To Pdb Format
... dimkal has provided me with a 3D strc of the compound. He has used Maestro to generate 3D from 2D file obtained in the above link given by neilfws. The structure looks fine (as we don't have maestro in our dept. I can't use that strc) but 1 of my friend in my institute suggested me to run optimizati ...
written 7.7 years ago by Tofayel Ahmed40
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Comment: C: Converting Sdf Format To Pdb Format
... I thank Wolf Ihlenfeldt, João Rodrigues, neilfws for their insightful replies. All the comments had addressed different practical issues and limitations in this case. ...
written 7.7 years ago by Tofayel Ahmed40
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Comment: C: Converting Sdf Format To Pdb Format
... yes, u r right.thanks. ...
written 7.7 years ago by Tofayel Ahmed40
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Converting Sdf Format To Pdb Format
... How to I convert a 2D sdf format file into a correct 3D pdb format structure (to be used in docking with a protein). The compound is Ruthenium Red and the wikipedia and Pubchem link is given below. Please take the complex structure of RR into account while giving suggestions, I mean how to handle th ...
format structure conversion written 7.7 years ago by Tofayel Ahmed40 • updated 7.7 years ago by Southwan30
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To Add All Or Only Polar Hydrogens
... Hello everybody, Got a simple doubt. Do I need to add all hydrogens or only polar hydrogens to my protein before doing energy minimization in SPDBViewer/DeepView? ...
written 7.9 years ago by Tofayel Ahmed40 • updated 5.7 years ago by João Rodrigues2.5k
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Comment: C: Rmsd Check B/W Native Crystal Conformation And Docked Conformation
... i just checked the server. i think its for aligning two protein pdb structures (can be template and modeled protein strc) and getting their rmsd value. i am still unable to do it. ...
written 7.9 years ago by Tofayel Ahmed40
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Rmsd Check B/W Native Crystal Conformation And Docked Conformation
... Can anybody suggest tools for checking RMSD difference b/w docked ligand conformation and its native conformation in the co-crystallized form. For information, I have separated ligand from protein obtained from PDB(thus generating apoproteins) and redocked in Autodock Vina, thus generating .pdbqt fi ...
protein docking written 7.9 years ago by Tofayel Ahmed40 • updated 7.9 years ago by João Rodrigues2.5k
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Comment: C: Fixing Amino Acid Residues In Disallowed Region
... Thanks for your concern. It is built by me via homology modeling. would definitely give a try in deepview. ...
written 7.9 years ago by Tofayel Ahmed40
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Comment: C: Fixing Amino Acid Residues In Disallowed Region
... Thank you Dr. Albert. The link sent by you answers it all. ...
written 7.9 years ago by Tofayel Ahmed40

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