-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
6,160 changed files
with
54,467 additions
and
12,294 deletions.
The diff you're trying to view is too large. We only load the first 3000 changed files.
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,2 @@ | ||
| <!DOCTYPE html><html><head><meta name='viewport' content='width=device-width, initial-scale=1'><meta name="description" content="A bioinformatic tool for identifying novel redox-active disulphide bonds in mammalian proteins, utilizing RCSB protein databank structures and providing a redox score."><meta name="keywords" content="ReDisulphID, bioinformatics, protein function, redox-active disulphides, covalent drugs, mammalian proteins, RCSB protein databank, redox score, HSE, solvent accessibility, pKa, disulphide bond prediction"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="robots" content="index, follow"><link rel='icon' type='image/png' href='icon.png'><link rel = 'stylesheet' href = 'style.css'><script src='3Dmol-min.js'></script><title>ReDisulphID</title></head><body><a href = 'list.html'><div class= 'title'>ReDisulphID<div class='subtitle'><p>a tool for identifying redox-active disulphides from structures</div></div></a><div class = 'main'> | ||
| <div class = 'menu'><a class = 'button' href = 'index.html'><div class= 'menuitem'>Home</div></a><a class = 'button' href = 'about.html'><div class= 'menuitem'>About</div></a><a class = 'button' href = 'list.html'><div class= 'menuitem'>List</div></a></div><h1>Menin</h1><div class = 'tabs'><div class = 'sep'>Intramolecular</div><a href = '#0' class = 'tablink'><div class = 'item' style='background:rgba(229.7297297297297,255,100,0.4);'>Cysteine 230 and cysteine 241</div></a></div><div class = 'tab'><div class = 'item structure' style='background:rgba(200, 200, 200, 0.4);;'><p class = 'struc' hidden>7o9x A 230 A 241 </p> <div style='height: 100%; position: relative;' class='viewer_3Dmoljs viewer' data-backgroundcolor='0xffffff' data-style='stick' data-ui='false'></div></div><div class = 'item redoxstatement' style='background:rgba(229.7297297297297,255,100,0.4);'>A redox-regulated disulphide may form within <b>Menin</b> at these cysteines. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. <a title = 'The redox score is related to how likely a cysteine pair is to form a redox active disulphide. It is calculated from solvent accessibility, pKa, and distance between each thiol in the cysteine pair. The highest redox score is 100.0, and the lowest redox score of a known redox-active intermolecular disulphide is 70.83, while the lowest score overall is 0.' class = 'help' href = 'about.html#scoreinfo'>?</a></div><h2>Details</h2><div class = 'grid'><div class = 'item infotitle'>Redox score <a title = 'The redox score is related to how likely a cysteine pair is to form a redox active disulphide. It is calculated from solvent accessibility, pKa, and distance between each thiol in the cysteine pair. The highest redox score is 100.0, and the lowest redox score of a known redox-active intermolecular disulphide is 70.83, while the lowest score overall is 0.' href = 'about.html#scoreinfo'>?</a></div><div class = 'item info'>55.5</div><div class = 'item infotitle'>PDB code</div><a class = 'link' target='_blank' rel='noopener' href = 'https://www.rcsb.org/structure/7o9x' ><div class = 'item info'>7o9x</div></a><div class = 'item infotitle'>Structure name</div><div class = 'item info'>crystal structure of human menin with fragment 16</div><div class = 'item infotitle'>Structure deposition date </div><div class = 'item info'>2021-04-17</div><div class = 'item infotitle'>Thiol separation (Å)</div><div class = 'item info'>9.95</div><div class = 'item infotitle'>Half-sphere exposure sum <a title = 'HSE is a measure of the accessibility of an amino acid side-chain. Cα atoms are counted in a 12 Å radius around the Cα of each cysteine in the potential redox-active disulphide bond. A lower HSE means an amino acid has fewer proximal amino acids, so is more accessible.' href = 'about.html#hseinfo'>?</a></div><div class = 'item info'>71</div><div class = 'item infotitle'>Minimum pK<sub>a</sub> <a title = 'The lowest pKa from each thiol in the cystiene pair. A lower minimum pKa means a cysteine pair is more likely to form a redox-regulated disulphide bond. The pKa of the cysteine thiols in the potential redox-active disulphide bond are calculated using the PROPKA algorithm.' href = 'about.html#pkainfo'>?</a></div><div class = 'item info'>12.29</div><div class = 'item infotitle'>% buried</div><div class = 'item info'>100</div><div class = 'item infotitle'>Peptide accession</div><a class = 'link' target='_blank' rel='noopener' href = 'https://www.uniprot.org/uniprotkb/A0A024R5E3/entry'><div class = 'item info'>A0A024R5E3</div></a><div class = 'item infotitle'>Residue number A</div><div class = 'item info'>230</div><div class = 'item infotitle'>Residue number B</div><div class = 'item info'>241</div><div class = 'item infotitle'>Peptide name</div><div class = 'item info'>Menin</div></div></div><div class = 'citation'>If this tool was useful for finding a disulphide, please cite: <p></div></div><script src='search.js'></script></body></html> | ||
| <!DOCTYPE html><html><head><meta name='viewport' content='width=device-width, initial-scale=1'><meta name="description" content="A bioinformatic tool for identifying novel redox-active disulphide bonds in mammalian proteins, utilizing RCSB protein databank structures and providing a redox score."><meta name="keywords" content="ReDisulphID, bioinformatics, protein function, redox-active disulphides, covalent drugs, mammalian proteins, RCSB protein databank, redox score, HSE, solvent accessibility, pKa, disulphide bond prediction"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="robots" content="index, follow"><link rel='icon' type='image/png' href='icon.png'><link rel = 'stylesheet' href = 'style.css'><script src="jquery-3.7.1.min.js"></script><script src='3Dmol-min.js'></script><title>ReDisulphID</title></head><body><a href = 'list.html'><div class= 'title'>ReDisulphID<div class='subtitle'><p>a tool for identifying redox-active disulphides from structures</div></div></a><div class = 'main'> | ||
| <div class = 'menu'><a class = 'button' href = 'index.html'><div class= 'menuitem'>Home</div></a><a class = 'button' href = 'about.html'><div class= 'menuitem'>About</div></a><a class = 'button' href = 'list.html'><div class= 'menuitem'>List</div></a></div><h1>Menin</h1><div class = 'tabs'><div class = 'sep'>Intramolecular</div><a href = '#0' class = 'tablink'><div class = 'item' style='background:rgba(255,146.829,100,0.4);'>Cysteine 230 and cysteine 241</div></a></div><div class = 'tab'><div class = 'item structure' style='background:rgba(200, 200, 200, 0.4);;'><p class = 'struc' hidden>7o9x A 230 A 241 </p> <div style='height: 100%; position: relative;' class='viewer_3Dmoljs viewer' data-backgroundcolor='0xffffff' data-style='stick' data-ui='false'></div></div><div class = 'item redoxstatement' style='background:rgba(255,146.829,100,0.4);'>A redox-regulated disulphide may form within <b>Menin</b> between cysteines 230 and 241. However, the redox score of this cysteine pair is lower than any known redox-active intermolecular disulphide. <a title = 'The redox score is related to how likely a cysteine pair is to form a redox active disulphide. It is calculated from solvent accessibility, pKa, and distance between each thiol in the cysteine pair. The highest redox score is 100.0, and the lowest redox score of a known redox-active intermolecular disulphide is 60, while the lowest score overall is 0.' class = 'help' href = 'about.html#scoreinfo'>?</a></div><h2>Details</h2><div class = 'grid'><div class = 'item infotitle'>Redox score <a title = 'The redox score is related to how likely a cysteine pair is to form a redox active disulphide. It is calculated from solvent accessibility, pKa, and distance between each thiol in the cysteine pair. The highest redox score is 100.0, and the lowest redox score of a known redox-active intermolecular disulphide is 60, while the lowest score overall is 0.' href = 'about.html#scoreinfo'>?</a></div><div class = 'item info'>29</div><div class = 'item infotitle'>PDB code</div><a class = 'link' target='_blank' rel='noopener' href = 'https://www.rcsb.org/structure/7o9x' ><div class = 'item info'>7o9x</div></a><div class = 'item infotitle'>Structure name</div><div class = 'item info'>crystal structure of human menin with fragment 16</div><div class = 'item infotitle'>Structure deposition date </div><div class = 'item info'>2021-04-17</div><div class = 'item infotitle'>Thiol separation (Å)</div><div class = 'item info'>10</div><div class = 'item infotitle'>Half-sphere exposure sum <a title = 'HSE is a measure of the accessibility of an amino acid side-chain. Cα atoms are counted in a 12 Å radius around the Cα of each cysteine in the potential redox-active disulphide bond. A lower HSE means an amino acid has fewer proximal amino acids, so is more accessible.' href = 'about.html#hseinfo'>?</a></div><div class = 'item info'>71</div><div class = 'item infotitle'>Minimum pK<sub>a</sub> <a title = 'The lowest pKa from each thiol in the cystiene pair. A lower minimum pKa means a cysteine pair is more likely to form a redox-regulated disulphide bond. The pKa of the cysteine thiols in the potential redox-active disulphide bond are calculated using the PROPKA algorithm.' href = 'about.html#pkainfo'>?</a></div><div class = 'item info'>12</div><div class = 'item infotitle'>% buried</div><div class = 'item info'>100</div><div class = 'item infotitle'>Peptide accession</div><a class = 'link' target='_blank' rel='noopener' href = 'https://www.uniprot.org/uniprotkb/A0A024R5E3/entry'><div class = 'item info'>A0A024R5E3</div></a><div class = 'item infotitle'>Residue number A</div><div class = 'item info'>230</div><div class = 'item infotitle'>Residue number B</div><div class = 'item info'>241</div><div class = 'item infotitle'>Peptide name</div><div class = 'item info'>Menin</div></div><h2>Ligandability</h2><h3>Cysteine 230 of Menin</h3><div class = 'grid'><div class = 'item ligandability '><p><a href = 'https://pubs.acs.org/doi/10.1021/jacs.1c11053' target='_blank' rel='noopener'>Not ligandable in the dataset of Yang <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202000870' target='_blank' rel='noopener'>Not ligandable in the dataset of Yan <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/nature18002' target='_blank' rel='noopener'>Not ligandable in the dataset of Backus <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1016/j.cell.2020.07.001' target='_blank' rel='noopener'>Not ligandable in the dataset of Vinogradova <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1021/acs.analchem.0c04726' target='_blank' rel='noopener'>Not ligandable in the dataset of Cao <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/s41587-020-00778-3' target='_blank' rel='noopener'>Not ligandable in the dataset of Kuljanin <i>et al.</i></a></p></div></div><h3>Cysteine 241 of Menin</h3><div class = 'grid'><div class = 'item ligandability '><p><a href = 'https://pubs.acs.org/doi/10.1021/jacs.1c11053' target='_blank' rel='noopener'>Not ligandable in the dataset of Yang <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202000870' target='_blank' rel='noopener'>Not ligandable in the dataset of Yan <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/nature18002' target='_blank' rel='noopener'>Not ligandable in the dataset of Backus <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1016/j.cell.2020.07.001' target='_blank' rel='noopener'>Not ligandable in the dataset of Vinogradova <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1021/acs.analchem.0c04726' target='_blank' rel='noopener'>Not ligandable in the dataset of Cao <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/s41587-020-00778-3' target='_blank' rel='noopener'>Not ligandable in the dataset of Kuljanin <i>et al.</i></a></p></div></div></div><div class = 'citation'>If this tool was useful for finding a disulphide, please cite: <p></div></div><script src='search.js'></script></body></html> |
Oops, something went wrong.