User: kazenokizi

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kazenokizi30
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30
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New User
Location:
United Kingdom
Last seen:
3 years, 3 months ago
Joined:
5 years, 9 months ago
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k*********@gmail.com

Posts by kazenokizi

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Ligand alignment to a fragment of a protein structure
... Hello. Thank you for the comment, but I am not sure molecular docking is what I am thinking. Say I have a segment of alpha helix, and I have a molecule which has similar number of atoms to the fragment, and its structure is a bit alike to the helix, though the molecule does not have amino acid in it ...
written 3.7 years ago by kazenokizi30
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Ligand alignment to a fragment of a protein structure
... Hello all, I am trying to align a ligand to a protein fragment using their pdb files. The two do not have the same number of atoms, neither do they have the same number of atoms of the same type. Sequence-based alignment is not successful in pymol or chimera, as the ligand does not have amino ...
chimera alignment pymol ligand command line written 3.7 years ago by kazenokizi30 • updated 3.7 years ago by Petr Ponomarenko2.6k
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How to retrieve PDB files based on text search
... Hello all, I would like to retrieve to my local machine all the x-ray allergen PDB files from RCSB pdb website/ftp based on text search 'allergen' via command line in Ubuntu. Is there a systematic way to do this? Cheers, Andrew ...
pdb allergen bash written 4.4 years ago by kazenokizi30
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Comment: C: Looking for pH-sensitive proteins
... Yes, I am looking for proteins which respond to pH changes by large conformational movement, but not into denaturation zone. I wonder whether there are some model proteins in which these responses are verified by experimental data, such as NMR, FRET, etc? ...
written 4.6 years ago by kazenokizi30
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Looking for pH-sensitive proteins
... Hello all, I am looking for pH-sensitive proteins as models to test a hypothesis for my computational design. Could you suggest some proteins, preferably with PDB structures? Thanks a lot. Andrew ...
ph protein sensitivity written 4.6 years ago by kazenokizi30 • updated 4.6 years ago by Michael Dondrup47k
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Drug design based on some residues of a protein
... Hello all, I have a question about drug design based on some residues of a protein. Bear with me since I have no training in computational drug design or anything related. I have identified some residues of a protein by a simulation method, and I would like to know how to design high specificity d ...
biochemistry drug design distal regulation written 4.7 years ago by kazenokizi30 • updated 2.1 years ago by RamRS30k
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Plant protein kinase of different classification but of similar structures?
... Hi all, I am new to plant protein kinase study, and I have been working on the differentiation of plant protein kinase function prediction. I am wondering how to find two protein kinases that look alike but function differently? I tried to look into PDB but there are too many entries to sort out st ...
next-gen written 5.8 years ago by kazenokizi30 • updated 5.8 years ago by Jean-Karim Heriche23k

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