source https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?resize=0&shownote=1&divid=div0&mmdbid=6m0j&date=20201222&command=view+annotations;+set+annotation+cdd;+set+view+detailed+view;+set+annotation+snp;+scap+interaction+6M0J_E_501_Y;+select+.E:501+%7C+name+snp_E_501;+line+graph+interaction+pairs+%7C+selected+non-selected+%7C+hbonds,salt+bridge,interactions,halogen,pi-cation,pi-stacking+%7C+false+%7C+threshold+3.8+6+4+3.8+6+5.5;+adjust+dialog+dl_linegraph;+select+displayed+set%7C%7C%7C%7B%22factor%22:%221.000%22,%22mouseChange%22:%7B%22x%22:%220.000%22,%22y%22:%220.000%22%7D,%22quaternion%22:%7B%22_x%22:%22-0.02596%22,%22_y%22:%22-0.6019%22,%22_z%22:%22-0.7910%22,%22_w%22:%22-0.1068%22%7D%7D
–
{
,
"structure0": {"id": "6M0J", "nodes1":[{"id":"N501.E.6M0J","r":"1_1_6M0J_E_501","s":"a","x":-34,"y":15,"c":"AAAAAA"}],
"nodes2":[{"id":"Y41.A.6M0J","r":"1_1_6M0J_A_41","s":"b","x":-38,"y":20,"c":"FF00FF"}, {"id":"K353.A.6M0J","r":"1_1_6M0J_A_353","s":"b","x":-32,"y":20,"c":"FF00FF"}, {"id":"G496.E.6M0J","r":"1_1_6M0J_E_496","s":"b","x":-40,"y":22,"c":"0000FF"}, {"id":"F497.E.6M0J","r":"1_1_6M0J_E_497","s":"b","x":-39,"y":18,"c":"0000FF"}, {"id":"Q498.E.6M0J","r":"1_1_6M0J_E_498","s":"b","x":-39,"y":15,"c":"0000FF"}, {"id":"P499.E.6M0J","r":"1_1_6M0J_E_499","s":"b","x":-38,"y":12,"c":"0000FF"}, {"id":"T500.E.6M0J","r":"1_1_6M0J_E_500","s":"b","x":-36,"y":12,"c":"0000FF"}, {"id":"G502.E.6M0J","r":"1_1_6M0J_E_502","s":"b","x":-30,"y":15,"c":"0000FF"}, {"id":"Y505.E.6M0J","r":"1_1_6M0J_E_505","s":"b","x":-31,"y":19,"c":"0000FF"}, {"id":"Q506.E.6M0J","r":"1_1_6M0J_E_506","s":"b","x":-33,"y":17,"c":"0000FF"}],
"links":[{"source":"N501.E.6M0J","target":"Q498.E.6M0J","v":13,"c":"0F0"}, {"source":"N501.E.6M0J","target":"P499.E.6M0J","v":13,"c":"0F0"}, {"source":"N501.E.6M0J","target":"G496.E.6M0J","v":13,"c":"0F0"}, {"source":"N501.E.6M0J","target":"Y505.E.6M0J","v":13,"c":"0F0"}, {"source":"N501.E.6M0J","target":"K353.A.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"T500.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"G502.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Q506.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Q498.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Y505.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Y41.A.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"P499.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"G496.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"F497.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Q498.E.6M0J","v":13,"c":"0F0"}, {"source":"N501.E.6M0J","target":"P499.E.6M0J","v":13,"c":"0F0"}, {"source":"N501.E.6M0J","target":"G496.E.6M0J","v":13,"c":"0F0"}, {"source":"N501.E.6M0J","target":"Y505.E.6M0J","v":13,"c":"0F0"}, {"source":"N501.E.6M0J","target":"K353.A.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"T500.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"G502.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Q506.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Q498.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Y505.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"Y41.A.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"P499.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"G496.E.6M0J","v":11,"c":"888"}, {"source":"N501.E.6M0J","target":"F497.E.6M0J","v":11,"c":"888"}]},
"structure1": {"id": "6M0J2", "nodes1":[{"id":"Y501.E.6M0J2","r":"1_1_6M0J2_E_501","s":"a","x":-34,"y":15,"c":"AAAAAA"}],
"nodes2":[{"id":"D38.A.6M0J2","r":"1_1_6M0J2_A_38","s":"b","x":-39,"y":24,"c":"FF00FF"}, {"id":"Y41.A.6M0J2","r":"1_1_6M0J2_A_41","s":"b","x":-38,"y":20,"c":"FF00FF"}, {"id":"K353.A.6M0J2","r":"1_1_6M0J2_A_353","s":"b","x":-32,"y":20,"c":"FF00FF"}, {"id":"G496.E.6M0J2","r":"1_1_6M0J2_E_496","s":"b","x":-40,"y":22,"c":"0000FF"}, {"id":"Q498.E.6M0J2","r":"1_1_6M0J2_E_498","s":"b","x":-39,"y":15,"c":"0000FF"}, {"id":"P499.E.6M0J2","r":"1_1_6M0J2_E_499","s":"b","x":-38,"y":12,"c":"0000FF"}, {"id":"T500.E.6M0J2","r":"1_1_6M0J2_E_500","s":"b","x":-36,"y":12,"c":"0000FF"}, {"id":"G502.E.6M0J2","r":"1_1_6M0J2_E_502","s":"b","x":-30,"y":15,"c":"0000FF"}, {"id":"Y505.E.6M0J2","r":"1_1_6M0J2_E_505","s":"b","x":-31,"y":19,"c":"0000FF"}, {"id":"Q506.E.6M0J2","r":"1_1_6M0J2_E_506","s":"b","x":-33,"y":17,"c":"0000FF"}],
"links":[{"source":"Y501.E.6M0J2","target":"Q498.E.6M0J2","v":13,"c":"0F0"}, {"source":"Y501.E.6M0J2","target":"P499.E.6M0J2","v":13,"c":"0F0"}, {"source":"Y501.E.6M0J2","target":"K353.A.6M0J2","v":19,"c":"F00"}, {"source":"Y501.E.6M0J2","target":"Y41.A.6M0J2","v":21,"c":"00F"}, {"source":"Y501.E.6M0J2","target":"Y41.A.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"Q498.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"P499.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"T500.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"G502.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"K353.A.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"Q506.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"Y505.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"G496.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"D38.A.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"Q498.E.6M0J2","v":13,"c":"0F0"}, {"source":"Y501.E.6M0J2","target":"P499.E.6M0J2","v":13,"c":"0F0"}, {"source":"Y501.E.6M0J2","target":"K353.A.6M0J2","v":19,"c":"F00"}, {"source":"Y501.E.6M0J2","target":"Y41.A.6M0J2","v":21,"c":"00F"}, {"source":"Y501.E.6M0J2","target":"Y41.A.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"Q498.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"P499.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"T500.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"G502.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"K353.A.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"Q506.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"Y505.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"G496.E.6M0J2","v":11,"c":"888"}, {"source":"Y501.E.6M0J2","target":"D38.A.6M0J2","v":11,"c":"888"}]}"structure0_common": {"id": "6M0J", "nodes1":[{"id":"N501.E.6M0J=>N501","r":"1_1_6M0J_E_501","s":"a","x":-34,"y":15,"c":"AAAAAA"}],
"nodes2":[{"id":"Y41.A.6M0J=>Y41","r":"1_1_6M0J_A_41","s":"b","x":-38,"y":20,"c":"FF00FF"}, {"id":"K353.A.6M0J=>K353","r":"1_1_6M0J_A_353","s":"b","x":-32,"y":20,"c":"FF00FF"}, {"id":"G496.E.6M0J=>G496","r":"1_1_6M0J_E_496","s":"b","x":-40,"y":22,"c":"0000FF"}, {"id":"F497.E.6M0J=>F497","r":"1_1_6M0J_E_497","s":"b","x":-39,"y":18,"c":"0000FF"}, {"id":"Q498.E.6M0J=>Q498","r":"1_1_6M0J_E_498","s":"b","x":-39,"y":15,"c":"0000FF"}, {"id":"P499.E.6M0J=>P499","r":"1_1_6M0J_E_499","s":"b","x":-38,"y":12,"c":"0000FF"}, {"id":"T500.E.6M0J=>T500","r":"1_1_6M0J_E_500","s":"b","x":-36,"y":12,"c":"0000FF"}, {"id":"G502.E.6M0J=>G502","r":"1_1_6M0J_E_502","s":"b","x":-30,"y":15,"c":"0000FF"}, {"id":"Y505.E.6M0J=>Y505","r":"1_1_6M0J_E_505","s":"b","x":-31,"y":19,"c":"0000FF"}, {"id":"Q506.E.6M0J=>Q506","r":"1_1_6M0J_E_506","s":"b","x":-33,"y":17,"c":"0000FF"}],
"links":[{"source":"N501.E.6M0J=>N501","target":"Q498.E.6M0J=>Q498","v":13,"c":"0F0"}, {"source":"N501.E.6M0J=>N501","target":"P499.E.6M0J=>P499","v":13,"c":"0F0"}, {"source":"N501.E.6M0J=>N501","target":"K353.A.6M0J=>K353","v":11,"c":"888"}, {"source":"N501.E.6M0J=>N501","target":"T500.E.6M0J=>T500","v":11,"c":"888"}, {"source":"N501.E.6M0J=>N501","target":"G502.E.6M0J=>G502","v":11,"c":"888"}, {"source":"N501.E.6M0J=>N501","target":"Q506.E.6M0J=>Q506","v":11,"c":"888"}, {"source":"N501.E.6M0J=>N501","target":"Q498.E.6M0J=>Q498","v":11,"c":"888"}, {"source":"N501.E.6M0J=>N501","target":"Y505.E.6M0J=>Y505","v":11,"c":"888"}, {"source":"N501.E.6M0J=>N501","target":"Y41.A.6M0J=>Y41","v":11,"c":"888"}, {"source":"N501.E.6M0J=>N501","target":"P499.E.6M0J=>P499","v":11,"c":"888"}, {"source":"N501.E.6M0J=>N501","target":"G496.E.6M0J=>G496","v":11,"c":"888"}]},
"structure1_common": {"id": "6M0J2", "nodes1":[{"id":"Y501.E.6M0J2=>N501","r":"1_1_6M0J2_E_501","s":"a","x":-34,"y":15,"c":"AAAAAA"}],
"nodes2":[{"id":"D38.A.6M0J2=>D38","r":"1_1_6M0J2_A_38","s":"b","x":-39,"y":24,"c":"FF00FF"}, {"id":"Y41.A.6M0J2=>Y41","r":"1_1_6M0J2_A_41","s":"b","x":-38,"y":20,"c":"FF00FF"}, {"id":"K353.A.6M0J2=>K353","r":"1_1_6M0J2_A_353","s":"b","x":-32,"y":20,"c":"FF00FF"}, {"id":"G496.E.6M0J2=>G496","r":"1_1_6M0J2_E_496","s":"b","x":-40,"y":22,"c":"0000FF"}, {"id":"Q498.E.6M0J2=>Q498","r":"1_1_6M0J2_E_498","s":"b","x":-39,"y":15,"c":"0000FF"}, {"id":"P499.E.6M0J2=>P499","r":"1_1_6M0J2_E_499","s":"b","x":-38,"y":12,"c":"0000FF"}, {"id":"T500.E.6M0J2=>T500","r":"1_1_6M0J2_E_500","s":"b","x":-36,"y":12,"c":"0000FF"}, {"id":"G502.E.6M0J2=>G502","r":"1_1_6M0J2_E_502","s":"b","x":-30,"y":15,"c":"0000FF"}, {"id":"Y505.E.6M0J2=>Y505","r":"1_1_6M0J2_E_505","s":"b","x":-31,"y":19,"c":"0000FF"}, {"id":"Q506.E.6M0J2=>Q506","r":"1_1_6M0J2_E_506","s":"b","x":-33,"y":17,"c":"0000FF"}],
"links":[{"source":"Y501.E.6M0J2=>N501","target":"Q498.E.6M0J2=>Q498","v":13,"c":"0F0"}, {"source":"Y501.E.6M0J2=>N501","target":"P499.E.6M0J2=>P499","v":13,"c":"0F0"}, {"source":"Y501.E.6M0J2=>N501","target":"Y41.A.6M0J2=>Y41","v":11,"c":"888"}, {"source":"Y501.E.6M0J2=>N501","target":"Q498.E.6M0J2=>Q498","v":11,"c":"888"}, {"source":"Y501.E.6M0J2=>N501","target":"P499.E.6M0J2=>P499","v":11,"c":"888"}, {"source":"Y501.E.6M0J2=>N501","target":"T500.E.6M0J2=>T500","v":11,"c":"888"}, {"source":"Y501.E.6M0J2=>N501","target":"G502.E.6M0J2=>G502","v":11,"c":"888"}, {"source":"Y501.E.6M0J2=>N501","target":"K353.A.6M0J2=>K353","v":11,"c":"888"}, {"source":"Y501.E.6M0J2=>N501","target":"Q506.E.6M0J2=>Q506","v":11,"c":"888"}, {"source":"Y501.E.6M0J2=>N501","target":"Y505.E.6M0J2=>Y505","v":11,"c":"888"}, {"source":"Y501.E.6M0J2=>N501","target":"G496.E.6M0J2=>G496","v":11,"c":"888"}]}"structure0_diff": {"id": "6M0J", "nodes1":[{"id":"N501.E.6M0J==>N501","r":"1_1_6M0J_E_501","s":"a","x":-34,"y":15,"c":"AAAAAA"}],
"nodes2":[{"id":"Y41.A.6M0J==>Y41","r":"1_1_6M0J_A_41","s":"b","x":-38,"y":20,"c":"FF00FF"}, {"id":"K353.A.6M0J==>K353","r":"1_1_6M0J_A_353","s":"b","x":-32,"y":20,"c":"FF00FF"}, {"id":"G496.E.6M0J==>G496","r":"1_1_6M0J_E_496","s":"b","x":-40,"y":22,"c":"0000FF"}, {"id":"F497.E.6M0J==>F497","r":"1_1_6M0J_E_497","s":"b","x":-39,"y":18,"c":"0000FF"}, {"id":"Q498.E.6M0J==>Q498","r":"1_1_6M0J_E_498","s":"b","x":-39,"y":15,"c":"0000FF"}, {"id":"P499.E.6M0J==>P499","r":"1_1_6M0J_E_499","s":"b","x":-38,"y":12,"c":"0000FF"}, {"id":"T500.E.6M0J==>T500","r":"1_1_6M0J_E_500","s":"b","x":-36,"y":12,"c":"0000FF"}, {"id":"G502.E.6M0J==>G502","r":"1_1_6M0J_E_502","s":"b","x":-30,"y":15,"c":"0000FF"}, {"id":"Y505.E.6M0J==>Y505","r":"1_1_6M0J_E_505","s":"b","x":-31,"y":19,"c":"0000FF"}, {"id":"Q506.E.6M0J==>Q506","r":"1_1_6M0J_E_506","s":"b","x":-33,"y":17,"c":"0000FF"}],
"links":[{"source":"N501.E.6M0J==>N501","target":"G496.E.6M0J==>G496","v":13,"c":"0F0"}, {"source":"N501.E.6M0J==>N501","target":"Y505.E.6M0J==>Y505","v":13,"c":"0F0"}, {"source":"N501.E.6M0J==>N501","target":"F497.E.6M0J==>F497","v":11,"c":"888"}]},
"structure1_diff": {"id": "6M0J2", "nodes1":[{"id":"Y501.E.6M0J2==>N501","r":"1_1_6M0J2_E_501","s":"a","x":-34,"y":15,"c":"AAAAAA"}],
"nodes2":[{"id":"D38.A.6M0J2==>D38","r":"1_1_6M0J2_A_38","s":"b","x":-39,"y":24,"c":"FF00FF"}, {"id":"Y41.A.6M0J2==>Y41","r":"1_1_6M0J2_A_41","s":"b","x":-38,"y":20,"c":"FF00FF"}, {"id":"K353.A.6M0J2==>K353","r":"1_1_6M0J2_A_353","s":"b","x":-32,"y":20,"c":"FF00FF"}, {"id":"G496.E.6M0J2==>G496","r":"1_1_6M0J2_E_496","s":"b","x":-40,"y":22,"c":"0000FF"}, {"id":"Q498.E.6M0J2==>Q498","r":"1_1_6M0J2_E_498","s":"b","x":-39,"y":15,"c":"0000FF"}, {"id":"P499.E.6M0J2==>P499","r":"1_1_6M0J2_E_499","s":"b","x":-38,"y":12,"c":"0000FF"}, {"id":"T500.E.6M0J2==>T500","r":"1_1_6M0J2_E_500","s":"b","x":-36,"y":12,"c":"0000FF"}, {"id":"G502.E.6M0J2==>G502","r":"1_1_6M0J2_E_502","s":"b","x":-30,"y":15,"c":"0000FF"}, {"id":"Y505.E.6M0J2==>Y505","r":"1_1_6M0J2_E_505","s":"b","x":-31,"y":19,"c":"0000FF"}, {"id":"Q506.E.6M0J2==>Q506","r":"1_1_6M0J2_E_506","s":"b","x":-33,"y":17,"c":"0000FF"}],
"links":[{"source":"Y501.E.6M0J2==>N501","target":"K353.A.6M0J2==>K353","v":19,"c":"F00"}, {"source":"Y501.E.6M0J2==>N501","target":"Y41.A.6M0J2==>Y41","v":21,"c":"00F"}, {"source":"Y501.E.6M0J2==>N501","target":"D38.A.6M0J2==>D38","v":11,"c":"888"}]}, linkmap: {
3: {"type": "peptidebond", "c":""},
4: {"type": "ssbond", "c":"FFA500"},
5: {"type": "ionic", "c":"0FF"},
6: {"type": "ionicInside", "c":"FFF"},
11: {"type": "contact", "c":"888"},
12: {"type": "contactInside", "c":"FFF"},
13: {"type": "hbond", "c":"0F0"},
14: {"type": "hbondInside", "c":"FFF"},
15: {"type": "clbond", "c":"006400"},
17: {"type": "halogen", "c":"F0F"},
18: {"type": "halogenInside", "c":"FFF"},
19: {"type": "pication", "c":"F00"},
20: {"type": "picationInside", "c":"FFF"},
21: {"type": "pistacking", "c":"00F"},
22: {"type": "pistackingInside", "c":"FFF"}
}}
Seen as a dataset, DNA is extremely flat (almost like white noise), therefore it’s not suitable to be used directly in artistic creation. In living organisms DNA is expressed through a wide range of mechanisms, determining what genes should be expressed, when, in what parts of the organism. Then the synthesis of proteins as amino acid chains follows chemical, magnetic and physics rules that determine the final product. And then again, the protein becomes part of a larger chemical mechanism in the specific part of the organism in order to execute its function (be it an enzyme, a hormone, structural, and so on).
In the experiments of DNA sonification I adopted a variety of techniques to interpret the DNA strands, not mimicking biological processes but somehow inspired by them. For example: using a dictionary of symbols similar to amino acids, reading DNA bases in triplets, using other data about the organisms like the DNA duplication speed or the genome size.
by Babak Mahjour, Jordan Bench, Rui Zhang, Jared Frazier, Tim Cernak
https://pubs.rsc.org/en/content/articlelanding/2023/dd/d3dd00008g
https://www.ncbi.nlm.nih.gov/Structure/icn3d/
– side chains: lines / sphere
– protein B-factor tube