- Last 7 days
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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
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pubs.acs.org pubs.acs.org
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n pools offive
every 5 compounds were put in a well
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Intact-Protein Mass Spectrometry
intact mass is used for screening
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993 mildly electrophilic fragment
993 compounds in the library
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covalent fragment screening
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- Mar 2020
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Local file Local file
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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
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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.
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Pharao
engine for pharmacophore matching
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eight comprehensive datasets
what are the datasets look like? this may help to understand the application domain of this tool.
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pharmacophores, heavyatoms or a combination of the two
pharmocophore or heavy atom match is used for measurement What does the score mean?
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better O3A alignments give higher scores
O3A alignment conformation generation, need to add Hs and use MMFF force field
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cg.cs.tsinghua.edu.cn cg.cs.tsinghua.edu.cn
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Jittor
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www.runoob.com www.runoob.com
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Online javascript editor
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antibodystructure.org antibodystructure.org
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antibody modeling
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ochem.eu ochem.eu
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A lot of data resources
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asteeves.github.io asteeves.github.io
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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?
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stackoverflow.com stackoverflow.com
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form["username"]
with Python 3.7.4, the statement should be:
form['username'].value
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stackoverflow.com stackoverflow.com
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python -m http.server --cgi 8000
use python to launch a http server
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www.mdanalysis.org www.mdanalysis.org
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MDAnalysis
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b
protonation state of the compound in panel b is wrong
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5FNQ9
this is the KEAP1 crystal structure used for virtual screening.
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Two of our top hits, iKeap1 and iKeap2 are able to displace the NFR2 peptide from KEAP1.
2 compounds can disrupt the PPI
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These compounds are shown in Supplementary Figs. 1, 2, and
Total 6 compounds
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using KEAP1 alone,
which PDB?
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the average docking score increase
top 50 molecules are selected. Although the average docking score increases, what about the average ligand efficiency
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AutoDock Vina
AutoDock Vina is the primary docking engine
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PDBQT
this is the input for AutoDock
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AutoDock
AutoDock is compatible with this tool
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10,000 CPU cores
10,000 CPU cores for 2 weeks Question:
- where can we find 10,000 CPU cores in China? AWS? Ali? Tencent?
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KEAP1
which PDB strcuture they chose?
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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.
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BVS)
the author will focus on SBVS, which mainly involves docking
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~1.3 billi
the 1.3 billion compounds consist of both Enamine REAL and ZINC
Tags
- wrong
- cloud computation
- virtual screening
- docking
- virtual library
- SBVS
- AutoDock
- AutoDock Vina
- question
Annotators
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www.rdkit.org www.rdkit.org
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legendFontSize
this can control the label size
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www.samson-connect.net www.samson-connect.net
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this tool seems like DataWarrior, and it uses RDkit
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Local file Local file
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After discussion with Xiao, I believe the tetramer hypothesis of TAZ-TEAD is not correct. Reasons:
- 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.
- 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.
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www.pnas.org www.pnas.org
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TAZ, but notYAP, could also form a homodimer
TAZ can form a homodimer, while YAP can't
Tags
Annotators
URL
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bmcchem.biomedcentral.com bmcchem.biomedcentral.com
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RD-Metabolizer
RD-Metabolizer used RDkit
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Developed by Honglin Li. Worth to check, since it is compared with SMARTCyp and seems to be better.
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lti-faceted roles in regulating tumorimmunity in addition to their growth-regulatory function
attention to its role in immune system should be paid
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www.cresset-group.com www.cresset-group.com
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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.
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2017Perspectivepubs
test
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France
It is a from french group.
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Miniperspective
this is a review
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- Dec 2019
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mp.weixin.qq.com mp.weixin.qq.com
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IPW
IPW may reverse brain aging by inhibit TGFbeta
Tags
Annotators
URL
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- Nov 2018
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STING
STING is abbreviation of stimulator of interferon genes
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- Mar 2017
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www.nature.com www.nature.com
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Alzheimer amyloid hypothesis lives on
test
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- Dec 2016
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www.nature.com www.nature.com
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Top 10
Nature Reviews Drug Discovery Top 10 is must to read
Tags
Annotators
URL
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- Nov 2016
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pubs.acs.org pubs.acs.org
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Cyclic Peptides
cellular permeable Peptide is very interesting
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hypothes.is hypothes.is
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AnnotatingAll Knowledge
This video is very good for new users to know the Hypothes.is is very welcome by the major publishers and why.
Tags
Annotators
URL
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www.nature.com www.nature.com
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Annotating the scholarly web
This is my 1st try of Hypothesis. And this article seems to sing high praise for this tool.
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