51 Matching Annotations
  1. Last 7 days
    1. distance between Lys37 on each H3 tail and the active site ofMLL1SETwas ~60 Å, allowing active-site access to H3 K4 and K9,but not to H3K27

      this distance betwen K37 and K4 may be similar to 60A, so that H3K4 methylation is possible



    1. n pools offive

      every 5 compounds were put in a well

    2. Intact-Protein Mass Spectrometry

      intact mass is used for screening

    3. 993 mildly electrophilic fragment

      993 compounds in the library

    4. covalent fragment screening

  2. Mar 2020
    1. ll datasets were supplied by Suther-land in the Supporting Information as 3D geometriesaligned according to the original literature, namely byflexible alignment on one or more templates obtained bycrystallographic enzyme-inhibitor complexes
    2. The scoring function was designed to encourage thematch between atoms with similar electrostatic charge,giving an additional bonus to atom pairs bearing a non-zeroformal charge of the same sign and a penalty to oppositelycharged centres

      the score will be high if atom with similar electrostatic charge is aligned.

    3. Pharao

      engine for pharmacophore matching

    4. eight comprehensive datasets

      what are the datasets look like? this may help to understand the application domain of this tool.

    5. pharmacophores, heavyatoms or a combination of the two

      pharmocophore or heavy atom match is used for measurement What does the score mean?



    1. GetDihedralConfDegree

      rdkit can measure dihedral. How to define the dihedral? seems user needs to provide 4 atom ids, but how to get the ids? Method 1. Use PyMOL to load the structure, and show label>Atom properties>Rank. Then the atom id will be labelled Method 2. Use SMARTS? How to?

    1. b

      protonation state of the compound in panel b is wrong

    2. 5FNQ9

      this is the KEAP1 crystal structure used for virtual screening.

    3. Two of our top hits, iKeap1 and iKeap2 are able to displace the NFR2 peptide from KEAP1.

      2 compounds can disrupt the PPI

    4. These compounds are shown in Supplementary Figs. 1, 2, and

      Total 6 compounds

    5. using KEAP1 alone,

      which PDB?

    6. the average docking score increase

      top 50 molecules are selected. Although the average docking score increases, what about the average ligand efficiency

    7. AutoDock Vina

      AutoDock Vina is the primary docking engine

    8. PDBQT

      this is the input for AutoDock

    9. AutoDock

      AutoDock is compatible with this tool

    10. 10,000 CPU cores

      10,000 CPU cores for 2 weeks Question:

      1. where can we find 10,000 CPU cores in China? AWS? Ali? Tencent?
    11. KEAP1

      which PDB strcuture they chose?

    12. ten drug

      The target the author chosen is a known target, with 10 drugs under clinical trials. So they have prior knowledge about the correct conformation of the binding site, and also the shape of the bound molecules. These helps a lot for the author to pick the hits.

    13. BVS)

      the author will focus on SBVS, which mainly involves docking

    14. ~1.3 billi

      the 1.3 billion compounds consist of both Enamine REAL and ZINC

    1. After discussion with Xiao, I believe the tetramer hypothesis of TAZ-TEAD is not correct. Reasons:

      1. There are two TAZ-TEAD binding modes in the structure, 5gn0. And one is similar to the canonical YAP-TEAD structure, albeit TAZ has shorter loop between the alpha helix and omega loop.
      2. the CoIP result just shows that TAZ can form homodimer, which is induced by its coiled-coil segment. And such coiled-coil segament is far from the TEAD binding domain.



    1. TAZ, but notYAP, could also form a homodimer

      TAZ can form a homodimer, while YAP can't

    1. lti-faceted roles in regulating tumorimmunity in addition to their growth-regulatory function

      attention to its role in immune system should be paid


    1. several conformation generation tools are compared, but the by comparing the RMSD between generated conformation and bioactive conformation is not quite reasonable. Instead, the rmsd of non-rotatable fragments should be the target.

  3. Dec 2019
  4. Nov 2018
    1. STING

      STING is abbreviation of stimulator of interferon genes


  5. Mar 2017
  6. Dec 2016
  7. Nov 2016
    1. AnnotatingAll Knowledge

      This video is very good for new users to know the Hypothes.is is very welcome by the major publishers and why.

    1. Annotating the scholarly web

      This is my 1st try of Hypothesis. And this article seems to sing high praise for this tool.