Comments for openlabnotebooks.org https://openlabnotebooks.org A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online Sun, 15 Oct 2023 21:05:29 +0000 hourly 1 https://wordpress.org/?v=5.5.18 Comment on A systematic review of drug-like ligands bound to helicases in the PDB by Lakshi Selvaratnam https://openlabnotebooks.org/a-systematic-review-of-drug-like-ligands-bound-to-helicases-in-the-pdb/#comment-30481 Thu, 29 Jun 2023 19:03:19 +0000 https://openlabnotebooks.org/?p=6608#comment-30481 In reply to Tim Willson.

Hi Tim,
I have compared the RecA-like domains of the helicases from this analysis and NSP13. I found that the pockets, where the inhibitors bind are, not conserved or similar to the RecA-like domains in NSP13. I will update again once I finish a complete analysis of the helicase domains from different superfamilies.

]]> Comment on A systematic review of drug-like ligands bound to helicases in the PDB by Tim Willson https://openlabnotebooks.org/a-systematic-review-of-drug-like-ligands-bound-to-helicases-in-the-pdb/#comment-29681 Tue, 30 May 2023 22:20:51 +0000 https://openlabnotebooks.org/?p=6608#comment-29681 Lakshi,
That’s a beautiful analysis of the known helicase ligands. It’s really interesting that so many of these inhibitors are allosteric and they appear to work by jamming up the motor rather than directly blocking the ATPase or unwindase activities. Do you find any common regions in or between the RecA domains that you think we should target based on your analysis of the X-ray crystal structures?
Tim

]]> Comment on Multiple Sequence Alignment and Phylogenetic Tree of Human and Viral Helicases by Holli-Joi Martin https://openlabnotebooks.org/multiple-sequence-alignment-and-phylogenetic-tree-of-human-and-viral-helicases/#comment-28592 Thu, 13 Apr 2023 15:17:59 +0000 https://openlabnotebooks.org/?p=6539#comment-28592 In reply to Lakshi Selvaratnam.

Interesting. Thanks so much for looking into this!

]]> Comment on Release of brachyury (TBXT) SPR Raw Data by Erica Rebouças https://openlabnotebooks.org/release-of-brachyury-tbxt-spr-raw-data/#comment-27419 Thu, 02 Mar 2023 20:12:36 +0000 https://openlabnotebooks.org/?p=6102#comment-27419 simplesmente uma Luz no fim do túnel, uma arma possivel contra o cordoma!! incrível!! parabéns aos cientistas envolvidos e Fundações de pesquisa contra o câncer!

]]> Comment on Multiple Sequence Alignment and Phylogenetic Tree of Human and Viral Helicases by Lakshi Selvaratnam https://openlabnotebooks.org/multiple-sequence-alignment-and-phylogenetic-tree-of-human-and-viral-helicases/#comment-27418 Thu, 02 Mar 2023 17:41:45 +0000 https://openlabnotebooks.org/?p=6539#comment-27418 In reply to Holli-Joi Martin.

Hi Holli-Joi,
I found that HSV (PDB ID P10189) is quite different from the other SF1 helicases. Here is the tree I’ve created with HSV highlighted: https://drive.google.com/file/d/1A4rAOpgbgGueQhyL4H_0ph-YHoEmYn1P/view?usp=share_link

]]> Comment on Multiple Sequence Alignment and Phylogenetic Tree of Human and Viral Helicases by Holli-Joi Martin https://openlabnotebooks.org/multiple-sequence-alignment-and-phylogenetic-tree-of-human-and-viral-helicases/#comment-26584 Tue, 31 Jan 2023 20:29:32 +0000 https://openlabnotebooks.org/?p=6539#comment-26584 I agree, this figure is great. Out of curiosity, where would the DNA helicase of the Human Herpes Virus would fit into this tree?

]]> Comment on Multiple Sequence Alignment and Phylogenetic Tree of Human and Viral Helicases by Lakshi Selvaratnam https://openlabnotebooks.org/multiple-sequence-alignment-and-phylogenetic-tree-of-human-and-viral-helicases/#comment-26553 Mon, 30 Jan 2023 17:11:40 +0000 https://openlabnotebooks.org/?p=6539#comment-26553 Hi Tim,
Unfortunately, there does not seem to be any inhibitors of human Upf1-like helicases.

]]> Comment on Identification of N-oxide containing helicase inhibitors by large-scale virtual screening by Anwar Hossain https://openlabnotebooks.org/identification-of-n-oxide-containing-helicase-inhibitors-by-large-scale-virtual-screening/#comment-26385 Thu, 26 Jan 2023 06:32:10 +0000 https://openlabnotebooks.org/?p=6514#comment-26385 In reply to Matthieu Schapira.

Hi Matthieu,
Thank you very much. We did docking at the third site of NSP13, “C-terminus-B.”

]]> Comment on Multiple Sequence Alignment and Phylogenetic Tree of Human and Viral Helicases by Tim Willson https://openlabnotebooks.org/multiple-sequence-alignment-and-phylogenetic-tree-of-human-and-viral-helicases/#comment-26377 Wed, 25 Jan 2023 20:26:31 +0000 https://openlabnotebooks.org/?p=6539#comment-26377 Beautiful work. From your sequence alignment, it appears that the human Upf1-like SF1 helicases are the closest to the viral SF1 helicases. Certainly much closer than any of the SF2 family helicases. Are there any known small molecule inhibitors of Upf1-like helicases?

]]> Comment on Identification of N-oxide containing helicase inhibitors by large-scale virtual screening by Matthieu Schapira https://openlabnotebooks.org/identification-of-n-oxide-containing-helicase-inhibitors-by-large-scale-virtual-screening/#comment-26372 Wed, 25 Jan 2023 15:56:48 +0000 https://openlabnotebooks.org/?p=6514#comment-26372 Anwar, congrats on this exciting work and on sharing your work-in-progress here. Could you maybe clarify which site of NSP13 was targeted in the virtual screening exercise?

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