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Messages - Phosphoserine

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1
DNA-protein interactions (SNAP) / Re: Unrecognized interactions
« on: April 12, 2017, 07:15:22 am »
Hi Xiang-Jun,

I'm afraid that I don't know of any papers specifically on this topic. I didn't really mean to pick out hydrophobic interactions specifically in the example, I was mostly interested in learning why I can't see them in the most general "List of X nucleotide/amino-acid interactions" section.

But you are right, if hydrogen bonding and stacking interactions are described in detail, it sounds like a good idea to also dedicate a section to contacts between hydrophobic carbon atoms. It would also be very useful to have a section on water-mediated interactions, which are also often crucial for the complex stability, but I understand this would probably involve a lot of additional work. But I'm afraid I don't have any advice on, for example, what inter-atomic distance cut-offs or angles between various vectors should be considered if one were to detect these (hydrophobic or water-mediated) interactions.

Best regards,
David

2
DNA-protein interactions (SNAP) / Re: Unrecognized interactions
« on: April 11, 2017, 07:49:02 am »
Hi,

thank you for the answer. Yes, adding the option --type=either helped recognize the interactions between the mentioned residues and DNA. If I understand correctly, the section "List of X nucleotide/amino-acid interactions" while using --type=either should include all interactions in the respective protein--DNA complex PDB structure which fall into the chosen inter-atomic distance cut-off ? And choosing --type=base or --type=backbone should report only the interactions of amino acid residues which interact with the DNA bases or DNA backbone, respectively, but not with the other one ?

It seems to me that only this one and the following (base-pair/amino-acid interactions) sections seem to be affected by the --type option. What confused me is that the following two sections which specifically deal with the backbone interactions (pair-wise phosphate-group/amino-acid H-bonding interactions and pair-wise sugar/amino-acid H-bonding interactions) are present in the .out file even when --type=base is selected, and, in fact, seem to be unaffected by the --type option. Similarly, the last three sections (base/amino-acid H-bonding interactions, base/amino-acid pseudo pairs, base/amino-acid pseudo stacks) are unaffected when one chooses --type=backbone.

This is just my opinion, but maybe some confusion could be prevented if the two sections dealing with the DNA backbone H-bonds and the last three sections describing interactions with DNA base atoms were either omitted when one chooses --type=base or --type=backbone, respectively, or if it were at least documented that they are agnostic to the --type setting. Alternatively, it would be helpful if it were documented that only the nucleotide/amino-acid interactions and base-pair/amino-acid interactions are affected by the --type option. From my (limited) experience, people are often interested in obtaining the complete list of interactions present in some protein--DNA complex, and it would be helpful to have it explicitly stated that the List of X nucleotide/amino-acid interactions section provides this (when --type=either is chosen).

Best regards,
David J.

3
DNA-protein interactions (SNAP) / Unrecognized interactions
« on: April 10, 2017, 10:24:59 am »
Dear Dr. Xiang-Jun,

I've recently compared the results of protein--DNA interaction analysis provided by 3DNA-SNAP to some (more primitive) analysis I did using my scripts. I've noticed that in some of the structures I was interested in the SNAP tool did not recognize some amino acid--nucleotide interactions, despite them containing inter-atomic distances shorter than the cut-off (4.5 A). See, for example, the structure 1TTU. Amino acids LYS 233, ARG 399, and VAL 403 are not mentioned in the .out file, despite each of them being involved in interactions with DNA residues in the 13-bp helix (there could also be others, I had used a shorter interaction cut-off in my analysis).

Is there any reason for omitting these interactions, or is it a bug ? Thought you might be interested in it.

Best regards,
David J.

4
DNA-protein interactions (SNAP) / Re: Segmentation fault
« on: May 21, 2016, 02:27:37 pm »
Dear Xiang-Jun,

thank you very much for the quick bug fix, the updated x64 Linux binary now runs without problems for virtually all protein--DNA complex structures there are available.

Best regards,
David J.

5
DNA-protein interactions (SNAP) / Segmentation fault
« on: May 21, 2016, 08:10:28 am »
Dear Dr. Xiang-Jun,

I have recently used the x64 Linux x3dna-snap binary to analyze the interactions in almost all available protein--DNA complexes, using the .pdb files as inputs. In over 3,700 of them, the program worked wonderfully, however, in four (PDB IDs 1LBG, 2VS7, 2VW9, 3T72) the program crashed with a segmentation fault. I was not able to observe any shared features in these complexes which could cause this unexpected behavior, nor do these complexes have any features which distinguish them from the structures for which the program worked (i.e., 1LBG is a C-alpha only structure, but the program did not crash for other CA structures).

This behavior was tested on Ubuntu 16.04 and Debian 8 machines and was reproduced under a Windows 10 environment with the .exe binary as well. Running the 32-bit Linux binary yields "program not found", so I can't test that. The web version of SNAP fails to process these structures as well.

It seems that it is beyond the scope of my knowledge to see what might be causing this behavior, but I thought you might appreciate this feedback and I hope it aids the development of this great tool.

Best regards,
David J.

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Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.