AlphaFold - Revision history

http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=AlphaFold AlphaFold - Revision history 2026-04-06T15:20:45Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=4115752&oldid=prev Joel L. Sussman at 09:40, 1 April 2024 2024-04-01T09:40:45Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:40, 1 April 2024</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In 2022, at [[CASP]] 15, AlphaFold2 continued to outperform all other methods in the majority of cases (see a summary of results at [[Theoretical_models#2022:_CASP_15|Theoretical models]]).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In 2022, at [[CASP]] 15, AlphaFold2 continued to outperform all other methods in the majority of cases (see a summary of results at [[Theoretical_models#2022:_CASP_15|Theoretical models]]).</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In September, 2023, John Jumper and Demis Hassabis received the Lasker Award for revolutionizing protein structure prediction<ref name="lasker-scientist">[https://www.the-scientist.com/news/lasker-award-for-revolutionizing-protein-structure-predictions-71386 Lasker Award for Revolutionizing Protein Structure Predictions], Laura Tran, <i>The Scientist</i>, September, 2023.</ref><ref name="lasker-nature">PMID: 37752227</ref>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In September, 2023, John Jumper and Demis Hassabis received the <ins style="color: red; font-weight: bold; text-decoration: none;">[https://laskerfoundation.org/winners/alphafold-a-technology-for-predicting-protein-structures </ins>Lasker Award<ins style="color: red; font-weight: bold; text-decoration: none;">] </ins>for revolutionizing protein structure prediction<ref name="lasker-scientist">[https://www.the-scientist.com/news/lasker-award-for-revolutionizing-protein-structure-predictions-71386 Lasker Award for Revolutionizing Protein Structure Predictions], Laura Tran, <i>The Scientist</i>, September, 2023.</ref><ref name="lasker-nature">PMID: 37752227</ref>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table style="background-color:#e0ffe0;border:1px solid black;font-size:120%;"><tr><td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table style="background-color:#e0ffe0;border:1px solid black;font-size:120%;"><tr><td></div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr></table></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr></table></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* See [https://www.ebi.ac.uk/training/online/courses/alphafold AlphaFold A practical Guide] Superb EMBL-EBI Interactive online <del style="color: red; font-weight: bold; text-decoration: none;">~3 hour </del>tutorial on AlphaFold2</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* See [https://www.ebi.ac.uk/training/online/courses/alphafold AlphaFold A practical Guide] Superb EMBL-EBI Interactive online tutorial on AlphaFold2 <ins style="color: red; font-weight: bold; text-decoration: none;">(~3 hours) </ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2</div></td></tr> </table>

Joel L. Sussman http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=4115751&oldid=prev Joel L. Sussman at 09:38, 1 April 2024 2024-04-01T09:38:09Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:38, 1 April 2024</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr></table></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr></table></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* See [https://www.ebi.ac.uk/training/online/courses/alphafold <del style="color: red; font-weight: bold; text-decoration: none;">EMBL-EBI Online Tutorail - </del>AlphaFold A practical Guide] <del style="color: red; font-weight: bold; text-decoration: none;">Super interactive </del>online ~<del style="color: red; font-weight: bold; text-decoration: none;">3h </del>tutorial on <del style="color: red; font-weight: bold; text-decoration: none;">AlphaFold</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* See [https://www.ebi.ac.uk/training/online/courses/alphafold AlphaFold A practical Guide] <ins style="color: red; font-weight: bold; text-decoration: none;">Superb EMBL-EBI Interactive </ins>online ~<ins style="color: red; font-weight: bold; text-decoration: none;">3 hour </ins>tutorial on <ins style="color: red; font-weight: bold; text-decoration: none;">AlphaFold2</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2</div></td></tr> </table>

Joel L. Sussman http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=4115750&oldid=prev Joel L. Sussman at 09:36, 1 April 2024 2024-04-01T09:36:19Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:36, 1 April 2024</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr></table></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr></table></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* See [https://www.ebi.ac.uk/training/online/courses/alphafold EMBL-EBI Online Tutorail - AlphaFold A practical Guide] Super interactive online ~3h tutorial on AlphaFold</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2</div></td></tr> </table>

Joel L. Sussman http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=4115749&oldid=prev Joel L. Sussman at 09:29, 1 April 2024 2024-04-01T09:29:08Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:29, 1 April 2024</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Hassabis_Demis.jpg|300px|right|thumb| Demis Hassabis - DeepMind]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Hassabis_Demis.jpg|300px|right|thumb| Demis Hassabis - DeepMind]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Jumper_John.jpg|300px|right|thumb| John Jumper - DeepMind]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Jumper_John.jpg|300px|right|thumb| John Jumper - DeepMind]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In 2020, the '''AlphaFold2'''<ref name="senior202001">PMID: 31942072</ref><ref name="alphafoldwikipedia">[https://en.wikipedia.org/wiki/AlphaFold AlphaFold] at Wikipedia.</ref> system of [https://deepmind.com DeepMind]<ref name="deepmindblog">[https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology AlphaFold: a solution to a 50-year-old grand challenge in biology], DeepMind Blog, November 30, 2020.</ref><ref name="deepmindwikipedia">[https://en.wikipedia.org/wiki/DeepMind DeepMind] at Wikipedia.</ref> demonstrated a '''major breakthrough'''<ref name="alquraishi">[https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ AlphaFold2 @ CASP14: “It feels like one’s child has left home.”] by Mohammed AlQuraishi, December 8, 2020.</ref><ref name="casppressrelease">[https://predictioncenter.org/casp14/doc/CASP14_press_release.html Artificial intelligence solution to a 50-year-old science challenge could ‘revolutionise’ medical research], CASP Press Release, November 30, 2020.</ref><ref name="callaway" /><ref name="helliwell">[https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14 DeepMind and CASP14] by John R. Helliwell, International Union of Crystallography Newsletter, December 4, 2020.</ref>. At [[Theoretical_models#2020:_CASP_14|CASP14]], AlphaFold2 was far better able, among over 100 competing groups, to '''predict structures, including sidechain positions''', so close to the subsequently revealed X-ray crystallographic structures as to differ by little more than the differences between two independently-determined X-ray structures of the same molecule. It did this for about two-thirds of the targets in the competition. AlphaFold2 has been hailed as '''largely solving the protein structure prediction problem for single-chain proteins'''<ref name="alquraishi" /><ref name="casppressrelease" /><ref name="callaway">PMID: 33257889</ref><ref name="helliwell" />. "Never in my life had I expected to see a scientific advance so rapid." said Mohammed AlQuraishi of Columbia University<ref name="alquraishi" />. But consider also "The joys and perils of AlphaFold"<ref name="perils">PMID: 34668287</ref>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In 2020, the '''AlphaFold2'''<ref name="senior202001">PMID: 31942072</ref><ref name="alphafoldwikipedia">[https://en.wikipedia.org/wiki/AlphaFold AlphaFold] at Wikipedia.</ref> system of [https://deepmind.com DeepMind]<ref name="deepmindblog">[https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology AlphaFold: a solution to a 50-year-old grand challenge in biology], DeepMind Blog, November 30, 2020.</ref><ref name="deepmindwikipedia">[https://en.wikipedia.org/wiki/DeepMind DeepMind] at Wikipedia.</ref> demonstrated a '''major breakthrough'''<ref name="alquraishi">[https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ AlphaFold2 @ CASP14: “It feels like one’s child has left home.”] by Mohammed AlQuraishi, December 8, 2020.</ref><ref name="casppressrelease">[https://predictioncenter.org/casp14/doc/CASP14_press_release.html Artificial intelligence solution to a 50-year-old science challenge could ‘revolutionise’ medical research], CASP Press Release, November 30, 2020.</ref><ref name="callaway" /><ref name="helliwell">[https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14 DeepMind and CASP14] by John R. Helliwell, International Union of Crystallography Newsletter, December 4, 2020.</ref>. At [[Theoretical_models#2020:_CASP_14|CASP14]], AlphaFold2 was far better able, among over 100 competing groups, to '''predict structures, including sidechain positions''', so close to the subsequently revealed X-ray crystallographic structures as to differ by little more than the differences between two independently-determined X-ray structures of the same molecule. It did this for about two-thirds of the targets in the competition. AlphaFold2 has been hailed as '''largely solving the protein structure prediction problem for single-chain proteins'''<ref name="alquraishi" /><ref name="casppressrelease" /><ref name="callaway">PMID: 33257889</ref><ref name="helliwell" />. "Never in my life had I expected to see a scientific advance so rapid." said Mohammed AlQuraishi of Columbia University<ref name="alquraishi" />. But consider also "The joys and perils of AlphaFold"<ref name="perils">PMID: 34668287</ref>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Joel L. Sussman http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=4115748&oldid=prev Joel L. Sussman at 09:28, 1 April 2024 2024-04-01T09:28:58Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:28, 1 April 2024</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><table align="right" width="180" style="border</del>:<del style="color: red; font-weight: bold; text-decoration: none;">1px solid black;margin</del>-<del style="color: red; font-weight: bold; text-decoration: none;">left</del>:<del style="color: red; font-weight: bold; text-decoration: none;">8px;"><tr><td></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image</ins>:<ins style="color: red; font-weight: bold; text-decoration: none;">Hassabis_Demis.jpg|300px|right|thumb| Demis Hassabis </ins>- <ins style="color: red; font-weight: bold; text-decoration: none;">DeepMind]]</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image</ins>:<ins style="color: red; font-weight: bold; text-decoration: none;">Jumper_John.jpg|300px|right|thumb| John Jumper - DeepMind]]</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> [[Image:Hassabis_Demis.jpg|300px|right|thumb| Demis Hassabis - DeepMind]]</div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Sameer velankar alphafold database for febs junior sections.jpeg]]</div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div></td></tr><tr><td></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[https://network.febs.org/videos/febs-junior-section-alphafold-database-webinar The AlphaFold Database in context] by Sameer Velankar and Gerard Kleywegt, EMBL-EBI, October 26, 2021. Hosted by [https://network.febs.org/rooms/junior-sections-of-febs-societies FEBS Junior Sections].</div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div></td></tr></table></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In 2020, the '''AlphaFold2'''<ref name="senior202001">PMID: 31942072</ref><ref name="alphafoldwikipedia">[https://en.wikipedia.org/wiki/AlphaFold AlphaFold] at Wikipedia.</ref> system of [https://deepmind.com DeepMind]<ref name="deepmindblog">[https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology AlphaFold: a solution to a 50-year-old grand challenge in biology], DeepMind Blog, November 30, 2020.</ref><ref name="deepmindwikipedia">[https://en.wikipedia.org/wiki/DeepMind DeepMind] at Wikipedia.</ref> demonstrated a '''major breakthrough'''<ref name="alquraishi">[https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ AlphaFold2 @ CASP14: “It feels like one’s child has left home.”] by Mohammed AlQuraishi, December 8, 2020.</ref><ref name="casppressrelease">[https://predictioncenter.org/casp14/doc/CASP14_press_release.html Artificial intelligence solution to a 50-year-old science challenge could ‘revolutionise’ medical research], CASP Press Release, November 30, 2020.</ref><ref name="callaway" /><ref name="helliwell">[https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14 DeepMind and CASP14] by John R. Helliwell, International Union of Crystallography Newsletter, December 4, 2020.</ref>. At [[Theoretical_models#2020:_CASP_14|CASP14]], AlphaFold2 was far better able, among over 100 competing groups, to '''predict structures, including sidechain positions''', so close to the subsequently revealed X-ray crystallographic structures as to differ by little more than the differences between two independently-determined X-ray structures of the same molecule. It did this for about two-thirds of the targets in the competition. AlphaFold2 has been hailed as '''largely solving the protein structure prediction problem for single-chain proteins'''<ref name="alquraishi" /><ref name="casppressrelease" /><ref name="callaway">PMID: 33257889</ref><ref name="helliwell" />. "Never in my life had I expected to see a scientific advance so rapid." said Mohammed AlQuraishi of Columbia University<ref name="alquraishi" />. But consider also "The joys and perils of AlphaFold"<ref name="perils">PMID: 34668287</ref>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In 2020, the '''AlphaFold2'''<ref name="senior202001">PMID: 31942072</ref><ref name="alphafoldwikipedia">[https://en.wikipedia.org/wiki/AlphaFold AlphaFold] at Wikipedia.</ref> system of [https://deepmind.com DeepMind]<ref name="deepmindblog">[https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology AlphaFold: a solution to a 50-year-old grand challenge in biology], DeepMind Blog, November 30, 2020.</ref><ref name="deepmindwikipedia">[https://en.wikipedia.org/wiki/DeepMind DeepMind] at Wikipedia.</ref> demonstrated a '''major breakthrough'''<ref name="alquraishi">[https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ AlphaFold2 @ CASP14: “It feels like one’s child has left home.”] by Mohammed AlQuraishi, December 8, 2020.</ref><ref name="casppressrelease">[https://predictioncenter.org/casp14/doc/CASP14_press_release.html Artificial intelligence solution to a 50-year-old science challenge could ‘revolutionise’ medical research], CASP Press Release, November 30, 2020.</ref><ref name="callaway" /><ref name="helliwell">[https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14 DeepMind and CASP14] by John R. Helliwell, International Union of Crystallography Newsletter, December 4, 2020.</ref>. At [[Theoretical_models#2020:_CASP_14|CASP14]], AlphaFold2 was far better able, among over 100 competing groups, to '''predict structures, including sidechain positions''', so close to the subsequently revealed X-ray crystallographic structures as to differ by little more than the differences between two independently-determined X-ray structures of the same molecule. It did this for about two-thirds of the targets in the competition. AlphaFold2 has been hailed as '''largely solving the protein structure prediction problem for single-chain proteins'''<ref name="alquraishi" /><ref name="casppressrelease" /><ref name="callaway">PMID: 33257889</ref><ref name="helliwell" />. "Never in my life had I expected to see a scientific advance so rapid." said Mohammed AlQuraishi of Columbia University<ref name="alquraishi" />. But consider also "The joys and perils of AlphaFold"<ref name="perils">PMID: 34668287</ref>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Joel L. Sussman http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=4115747&oldid=prev Joel L. Sussman at 09:26, 1 April 2024 2024-04-01T09:26:03Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:26, 1 April 2024</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table align="right" width="180" style="border:1px solid black;margin-left:8px;"><tr><td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table align="right" width="180" style="border:1px solid black;margin-left:8px;"><tr><td></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> [[Image:Hassabis_Demis.jpg|300px|right|thumb| Demis Hassabis - DeepMind]]</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Sameer velankar alphafold database for febs junior sections.jpeg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Sameer velankar alphafold database for febs junior sections.jpeg]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr><tr><td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr><tr><td></div></td></tr> </table>

Joel L. Sussman http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=4115746&oldid=prev Joel L. Sussman at 09:22, 1 April 2024 2024-04-01T09:22:44Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:22, 1 April 2024</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table align="right" width="180" style="border:1px solid black;margin-left:8px;"><tr><td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table align="right" width="180" style="border:1px solid black;margin-left:8px;"><tr><td></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Hassabis_Demis.jpg Demis Hasabis of DeepMind]]</div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Sameer velankar alphafold database for febs junior sections.jpeg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Sameer velankar alphafold database for febs junior sections.jpeg]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr><tr><td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr><tr><td></div></td></tr> </table>

Joel L. Sussman http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=4115745&oldid=prev Joel L. Sussman at 09:21, 1 April 2024 2024-04-01T09:21:15Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:21, 1 April 2024</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table align="right" width="180" style="border:1px solid black;margin-left:8px;"><tr><td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><table align="right" width="180" style="border:1px solid black;margin-left:8px;"><tr><td></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Hassabis_Demis.jpg Demis Hasabis of DeepMind]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Sameer velankar alphafold database for febs junior sections.jpeg]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Sameer velankar alphafold database for febs junior sections.jpeg]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr><tr><td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr><tr><td></div></td></tr> </table>

Joel L. Sussman http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=3974856&oldid=prev Eric Martz: /* See Also */ 2023-11-30T19:08:30Z

<p><span class="autocomment">See Also</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 19:08, 30 November 2023</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 93:</td> <td colspan="2" class="diff-lineno">Line 93:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>- ColabFold: A [https://www.youtube.com/watch?v=Rfw7thgGTwI video covering an overview, comparison of some of the methods and how people are already extending them, how to submit and interpret, and a tutorial on how to use AlphaFold2 Colab] is available. The video was recorded on August 4th, 2021 presented by Sergey Ovchinnikov and Martin Steinegger, hosted by Chris Bahl for the Boston Protein Design and Modeling Club</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>- ColabFold: A [https://www.youtube.com/watch?v=Rfw7thgGTwI video covering an overview, comparison of some of the methods and how people are already extending them, how to submit and interpret, and a tutorial on how to use AlphaFold2 Colab] is available. The video was recorded on August 4th, 2021 presented by Sergey Ovchinnikov and Martin Steinegger, hosted by Chris Bahl for the Boston Protein Design and Modeling Club</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==Advances since 2021==</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*RoseTTAFoldNA<ref>PMID: 37996753</ref> offers a leap forward in predicting structures of complexes of proteins and nucleic acids, but in November 2023 is not yet available as a free server.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See Also==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See Also==</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=AlphaFold&diff=3947663&oldid=prev Eric Martz at 16:48, 11 November 2023 2023-11-11T16:48:58Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 16:48, 11 November 2023</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* If a prediction is already in the [[#AlphaFold Database of Predictions|AlphaFold Database]], simply download it.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* If a prediction is already in the [[#AlphaFold Database of Predictions|AlphaFold Database]], simply download it.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Otherwise, follow [[How to predict structures with AlphaFold]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Otherwise, follow [[How to predict structures with AlphaFold]].</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Uploading the predicted PDB file to [http://FirstGlance.Jmol.Org FirstGlance in Jmol] will automatically '''color it by estimated reliability per residue'''. Examples: [http://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Snapshot], [http://firstglance.<del style="color: red; font-weight: bold; text-decoration: none;">molviz</del>.org/fg.htm?mol=AF-Q9AY27-F1-model_v1.pdb Interactive].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Uploading the predicted PDB file to [http://FirstGlance.Jmol.Org FirstGlance in Jmol] will automatically '''color it by estimated reliability per residue'''. Examples: [http://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Snapshot], [http://firstglance.<ins style="color: red; font-weight: bold; text-decoration: none;">jmol</ins>.org/fg.htm?mol=AF-Q9AY27-F1-model_v1.pdb Interactive].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr></table></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></td></tr></table></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Eric Martz