397 Matching Annotations
  1. Jan 2022
    1. The on-resonance frequency needs to be optimized for each protein

      How to optimize it? How to measure if the frequency is good enough? on-resonance frequency from -3~0 ppm

  2. Dec 2021
    1. only about 1% of carbon atoms are C-13. These are the only ones picked up by this form of NMR. If you had a single molecule of ethanol, then the chances are only about 1 in 50 of there being one C-13 atom in it, and only about 1 in 10,000 of both being C-13. But you have got to remember that you will be working with a sample containing huge numbers of molecules. The instrument can pick up the magnetic effect of the C-13 nuclei in the carbon of the CH3 group and the carbon of the CH2 group even if they are in separate molecules. There's no need for them to be in the same one.

      the author believe that even though the percentage of C-13 is low, but its NMR signal can be captured.

    2. About 1% of all carbon atoms are the C-13 isotope

      So 13C NMR do not need to use C-13 for synthesis?

  3. Nov 2021
    1. despite of the enormous efforts being devoted, it remains to be a huge challenge to improve the biocompatibility and reduce the side effect of silver

      silver can interact with human protein and DNA

    2. Those structures reveal that Ag+ binds to 6PGDH at both catalytic and non-catalytic sites with dominant binding residues of Cys, His and Met in quasi-linear and trigonal geometry, which is generally consistent with our previous reports36,40. Together with the site-directed mutagenesis study, we unveil that Ag+ abolishes the enzymatic activity of 6PGDH through targeting His185 in the active site and morphing its catalytic pocket.

      Ag can bind with protein at Cys, His and Met residues.

    1. silver sulfadiazine on bacteria differs from silver nitrate and sodium sulfadiazine

      what is the difference?

  4. Oct 2021
    1. In contrast, Bcr-Abl is found to localize exclusively in the cytoplasm where it can be positioned in proximity to the signaling proteins controlled by its activated kinase domain.

      Bcr-abl is located in cytoplasm

    1. --pc+

      this function seems to be similar to the one mentioned in the following paper https://aip.scitation.org/doi/full/10.1063/1.4914315

    2. 1.001

      %VERSION VERSION_STAMP = V0001.001 DATE = 12:05:14 00:09:29 above text is the actual text in an XVV file

    3. All of these corrections havebeen almost exclusively used with pure water under ambient condition

      these correction methods are more compatible with pure water so far.

    4. in order

      one after the previous one

    5. closure name

      example: "kh,pse2,pse3"

    6. molReconstruct

      add this option does not output a pdb file with water molecules inside. it will add the density of both H and O, thus generate a new density file, the "molecular density"

    7. excess chemical potential

      https://en.wikipedia.org/wiki/Excess_chemical_potential this concept should be similar to free energy

    8. Parameters

      1D-RISM input file parameters

    9. Both sander and NAB have MPI implementations of 3D-RISM

      3D-RISM is only available in sander and NAB, and MPI is supported

    10. Calculating a 3D-RISM solution for a single solute conformation typically requires about 100 times more com-puter time than the same calculation with explicit solvent or PB

      3D-RISM is slow than explicit solvent calculation.

    11. molReconstruct

      water can be reconstructed by setting molReconstruct, but how?

    12. 1D-RISM may be usedto treat solutions of aqueous alkali and halide ions at various concentration

      So salt can be added during 1D-RISM

    13. accelerated by the modified direct inversion of the iterative subspace (MDIIS)

      MDIIS is used during 1D-RISM calculation

    14. A dielectrically consistent version of 1D-RISM theory (DRISM) e


    15. an approximate closure relation must beused. While many closures have been developed, at this time only three are implemented in 3D-RISM:

      HNC, KH and PSE-n are 3 approximate closure relations implemented in Amber



    1. water

      water placed by crystallographers may not represent the true picture of solvation structure

    2. independent gradient model

      similar to NCI plot


    1. translate thecontinuous distributions from 3D-RISM calculations to explicitones, furthering the usefulness of 3D-RISM

      aim of this paper


    1. Under most circumstances, only PrP molecules with an identical amino acid sequence to the infectious PrPSc are incorporated into the growing fiber

      only PrP molecules with an identical sequence to the PrPSc can be recruited to the fiber

  5. Sep 2021
    1. Protein and the dye were mixed in 1:1 volume ratio

      such volume ratio will lead to excessive protein conc.?

    2. 300 counts at a LED power of 50 %

      300 counts fluorescence is needed.

    3. lysis of bacterial cells containing no His6-pUL53 was produced for the dilution series in buffer

      this might be the mock lysate

    4. RED-tris-NTA

      his tag can be labeled in lysate

    5. The concentration of His6-pUL53 was estimated based on the previous experiences with the purification yields.

      concentration is estimated here. How does the author estimate?

    6. photobleaching

      Photobleaching is the chemical alteration of the indicator dye, be it a fluorophore or a colorimetric dye, so that it is unable to fluoresce due to the destruction of covalent or non-covalent bonds due to non-specific binding caused by excitation light.

    7. ST-optimized NT-647 dye (RED-tris-NTA).

      NT-647 is not available now. NT-647 is a red dye.

    8. because of its small size, binding of tris-NTA has minimum effect on biochemical and physicochemical properties of the protein

      small tag may not alter the conformation and function of the protein

    9. The observed Kd values were 1.3 ± 0.2 nM for the His6 peptide, 0.6 ± 0.3 nM for IDH R132H and 2.4 ± 1.1 nM for p38α

      2 points:

      1. binding Kd is about 1nM
      2. Kd for different targets could be slightly different



    1. WIGSRHWEX641

      The Eppendorf MixMate can run at 2000 RPM. but 15s mixing is not enough, 60s seems enough


      solution will splash when the rotation speed increase to 2300 RPM

    1. this paper described some hit compounds that interfere with the assay components. some compounds react with thiol, and their SAR is reported.

    2. We were also aware that this method is subject to assay interference by thiol-containing compounds

      this assay involves a thiol intermediate, so it will be interfered by thiol containing compounds, or compounds that react with thiol group. But common HTRF will not be affected.

    3. ALARM NMR

      what is this tech?

    4. Significant resources in early drug discovery are spent unknowingly pursuing artifacts and promiscuous bioactive compounds

      PAINS=artifacts and promiscuous bioactive compounds

    1. EPSPS

      what is the function of this gene? what is the metabolite of this protein? will it be digested in rat stomach? any idea how this gene affected rat?

    2. GMO

      genetically modified orgnisms

    3. rats

      what rat?



  6. Aug 2021
    1. there are gaps in our current knowledge that are essential to fill in order for us to fully understand the clinical implications of targeting this pathway both in terms of clinical efficacy and safety.


    1. however, it also led to some level of cell membrane damage

      the merged peptide led to some level of cell membrane damage

    2. Conjugation of our cyclic peptide at the C-terminal with cell penetrating peptide like TAT enabled cell penetrating

      cell penetrating peptide TAT conjugated with a peptide binder

    1. Incubation at 4 degrees Cel-sius and other temperatures are often more stable since the incubation is performed in some type of incubator.

      Crystallization at 4 degree is carried out in an incubator.

    1. Nearly 2.4 million small molecules were screened using the SDF files of compound libraries from ChemDiv (San Diego, CA) and Timtec (Newark, DE).

      ChemDiv library of 2.4 million compounds were screened

    2. 3DWH

      protein model for docking

    1. GPCRs and proteases

      GPCR and proteases were used as model system

    2. 96 fragment-sized compounds (SpotXplorer0)

      what compounds is included?

    1. t is interesting that the F2X-Entry library gave considerably higher hit rates than the second 96-compound library, albeit on different targets.

      F2X-entry seems to be better than the Klebe's library in hit rate.

    2. crystallography has become the most popular technique for FBLD

      FBDD by crystallography is most popular from 2019

  7. Jul 2021
    1. In a pull-down assay, a bait protein is tagged and captured on an immobilized affinity ligand specific for the tag, thereby generating a "secondary affinity support"’ for purifying other proteins that interact with the bait protein

      basics of pull-down assay

    1. These experiments were performed much faster and efficiently when compared to traditional SDS-PAGE

      Tycho is used to replace SDS-page

  8. Jun 2021
  9. May 2021
    1. DMSO has high heats of dilution and should be matched extremely well between the cell and the syringe


    2. The two binding partners must be in identical buffersto minimize heats of dilution

      must be in identical buffer to minimize dilution heat

    1. FLEV this residue"

      I tested this function in Coot 0.9.5 Linux, but never succeeded!!!

    1. 20 targets for validation that we narrowed down to one novel intracellular target

      one out of 20 targets was selected for further study. The target is an intracellular target, but the target is not disclosed.

    2. The target novelty and disease association scoring was assessed by a natural language processing (NLP) engine, which analyses data from millions of data files, including patents, research publications, grants, and databases of clinical trials

      Method and data In Silico used for target identification

    1. ∼30 μM

      thermal shift EC50 of thalidomide is 30 uM. However, such EC50 is not equivalent to binding affinity

    2. bead assay to measure compound binding

      How does this assay work?

    1. ProMod3 uses the OpenMM library (Eastman et al.) to perform the computations and the CHARMM22/CMAP force field (Mackerell et al.) for parameterisation

      Homology model built by SwissModel is minimized by OpenMM

  10. Apr 2021
  11. Mar 2021
    1. The thermophoresis of a fluorescently labeled molecule A

      fluorescent label is needed? here the molecule A is protein or ligand?

    1. LE

      Ligand Express, the 1st generation tool by Cyclica

    2. chMaker, a deep learning algorithm that synthetically augments the millions of known DTIs found in public databases with biophysical information from 3D structure databases.

      deep learning + 3D protein structure

  12. Dec 2020
    1. an expert in fragment-based and covalent drug discovery.

      FBDD expert

    2. Chief Scientific Officer of Arvinas

      a senior industry leader

    3. Johannes holds a Ph.D. in quantum & molecular mechanics

      he is a CADD Ph. D

    4. data science expert

      data science expert

    5. global Head for Data Science at Johnson & Johnson Medical Devices Technology

      a senior industry leader

    6. Vice President of Oncology Research at AstraZeneca

      Kevin is a senior industry leader

    7. DANIEL K. NOMURA, Ph.D.

      Nomura is collaborting with Novartis to identify covalent binders. Novartis provide CADD and chemical library

  13. Nov 2020
    1. Journal of the American Chemical Society. 2018, 140, 8069-8073.

      covalent warhead

  14. Oct 2020
    1. From the molecules in the candidate pool find the one that has the maximum value for its minimum distance to molecules in the picked set (hence the MaxMin name), calculating and recording the distances as required. This molecule is the most distant one to those already picked so is transferred to the picked set.

      a good summary of MaxMin method

    1. This furyl amide series was of particular interest due to its starting potency, modular nature, structural properties and absence of reactive functionality found within typical covalent modifiers.

      they are seeking for non-covalent inhibitors.

  15. Aug 2020
    1. In situations where Greek letters are unavailable (for example, on some computer displays), they may be replaced by upper case Roman letters (a = A, p = B, 7 = G, d = D, E = E, 4 = Z, 17 = H).

      hydrogen atom nomencleture by IUPAC

    1. their structure formed by interrelated dimeric polypeptide chains

      TGF beta forms dimer to bind with TGF beta receptor. Homodimers are reported for beta 1 and 2; does heterodimer exists?

    1. Generally the intensity of the detected STD-NMR signal depends not only on the efficiency of the receptor-to-ligand saturation transfer but also on the number of ligand molecules in solution that received saturation from the receptor. Because ligand exchange is in place during the saturation time, long saturation times (up to 3 seconds)8 or high ligand excess (10 to 100 fold), allow transfer of saturation from one receptor molecule to much more than one molecule of ligand.

      this is a very vivid description of the saturation exchange process.

    2. Normally, for a determinate system the ligand-to-protein ratio and the saturation time have to be selected according to the expected KD

      useful hint


    1. only the signals of the hydrogens that are in closecontact to the protein (e5 Å) and receive magnetization transfer

      2 factors lead to saturation transfer: 1. close in space 2. receive magnetization transfer

    2. This value is about 10 times higher than thevalue reported in literature for this system

      Kd determination by STD may not be accurate with the method mentioned in this paper



    1. Thecovalentinhibitordisplayeda5-foldincreasein cellularactivitycomparedto the reversiblecounterpart

      cellular activity improvement

    2. To stabilizethe readilyreversiblealdimineadduct,anortho-boronicacidgroupwas included

      aldehyde forms reversible adduct with lysine. attention

    3. 5MKS

      the covalent bond is missing in the release structure.

    4. Theirreversiblecovalentinhibitor29displayedsuperiorcellularactivitycomparedtoits reversiblecounterpart

      what is the cellular activity of both compounds? In fact, NU6300's binding to CDK2 is weaker than NU6102, and inhibition of Rb phosphoralytion at 50 uM is weaker too. However, its residense time is longer.

    5. N-a-acetyl-lysine



    1. however, there was noevidence of covalent bonding to the protein.

      this result is similar to CNIBR result, thus it is important to assess the cysteine reactivity before any MedChem efforts.



    1. owever, neither of these two new compounds appeared to form a covalent bond with Cys481 in our crystal structures

      covalent warhead does not attach to cysteine


    1. the typical concentrations of protein and ligand are 2.0–20μM and0.2–2.0 mM, respectively, the ranges of which may depend on solubility of the chemical compounds inwater or available amounts of both interacting partners

      typical concentration: protein 2~20 uM ligand 0.2~2 mM ratio: 1:100

    2. NOE-Based Methods

      STD is one of the NOE based methods

    3. NMR in SBDD review

    4. Ligand-based NMR approaches have limitations with respect to the exchange rate between thetarget protein and ligand compound

      slow off ligand will not reflect the binding event



    1. the presence of large excess of ligand, the satu-ration of free ligands in solution gets amplified because the relaxation of small molecules is slower than the saturation transfer.



    1. This is in agreementwiththe lackof slowlyexchangingpolarresiduesin the CTBbindingpocket

      So D2O/H2O differential STD will highlight the slow exchange polar protein H

    2. use of solventsuppression

      How to do this?

    3. aromaticproteinspectralregions

      if compound contains aryl ring, this frequency should not be used to saturate the system, then how should we choose this frequency?

    4. theseproton

      proton of polar residues

    5. Anothersourceof minordifferencesinepitopemapsisthesolven

      Hydrogen atoms of polar residues will be exchanged to Deuterium when solvent is D2O. In contrast, they will not excha

    6. incethefrequenciesof irradiationcan be chosen,we can selectwhattypesof proteinprotonswill be “directlyirradiated”,so thatthe differenceswill highlightpartsof the ligandcontactingthosetypesof proteinresiduesin the boundstate

      different irradiation frequency will highlight different parts of the types of protein residues that contact with ligand.


    1. x 64

      what does this mean? count of detections?

    2. WhichDSTD values should be considered significantwill depend on the sizes of the STD factors for the protein-ligand system under study

      delta STD cutoff needs to be determined according to the system tested.

    3. Y525, which is known to have a very fast kinetics of exchange

      this is measured previously

    4. the 3D structure of the protein can be used to predict the chemical shifts using existing software

      which software can predict the NMR of protein? ShiftX2

    5. protonated residues within 4 Å

      4 A?

    1. 100%D2O

      100% D2O is needed, to allow sufficient STD to ligand and not water or other solvent.

    2. SaturationtransferNMRwasapioneeringtechniquedevelopedin1979

      STD was used first in 1979


    1. wereobtainedbycollecting128scans

      number of scans can be accumulated?

    2. nfact,thereisanincreaseofsensitivitywiththesizeofproteinduetoamoreefficientinter-andintramolecularsaturationtransfer

      larger size of protein will increase the sensitivity due to more efficient inter- and intramolecular saturation transfer

    3. Usinghigherfieldspectrometerswillmakethemethodevenmoreefficientsincesensitivityandspindiffusionincreasewithfieldstrength

      higher field strength will help increase the sensitivity

    4. wheatgermagglutinin
    5. thedegreeofsaturationofligandsdependsonthesizeoftheprotein,theoffset,andthedurationoftheon-resonanceirradiation,thedissociationrateconstantkoff,andtheexcessofligand

      the degree of saturation of ligands depends on the size of the protein, the offset, and the duration of the on-resonance irradiation, the dissociation rate constant koff, and the excess of ligand

    6. highturnoverratesresultinalargereffectathigherligand-to-proteinratios.SlowdissociationrateswillyieldsmallerSTDNMRsignalsand,thus,reducesensitivity

      Slow dissociation rates will yield smaller STD NMR signals and, thus, reduce sensitivity



    1. nn8

      number of entries on line

    2. Substitution Count [Query]

      substitution count


  16. Jul 2020
    1. restrictingligandconformationalflexibilityacceleratedthebinding

      conformation is related to kon

    2. seriesofagonistsoftheA2Aadenosinereceptor

      really? I need to check the original data.

    3. narrowpassageway

      How to define is a passageway is narrow or not?

    4. diffusion-limitedon-rate(kon109M1s1)

      this should be the maximum kon, right?



    1. the key method for conformation comparison used in this artical is wrong, so the result is not very informative.

    2. As shown in Appendix B, for the specific case of AMP, we could have reducedthe computational cost grossly by one order of magnitude

      100 us is enough?

    3. For the purpose of comparing the features of the conformational ensemble extracted from ourMD simulations (plain and replica-exchange) to the structures generated by conformer generators(vide infra), we performed a symmetric root mean square displacement-based cluster analysis using thehierarchical agglomerative algorithm

      clustering is used to compare conformations

    4. AMBERTOOLS14[59] adopting GAFFparameters [42] for the molecule and the TIP3P model of water

      GAFF for LMW, TIP3P water

    5. GAUSSIAN09

      commercial QM tool

    6. performs slightly better than some widely-used conformer generation tools when considering boththe abilities to generate high-diversity conformational ensembles and to reproduce experimentally theavailable structures

      plain MD sampled slightly better diverse conformational space than conformer generation tools

    7. (i) consistent with that obtained from REMD simulations

      plain MD sampled similar conformational space as REMD How they measured?



    1. PD3.1)

      How did they find it? 1st round: They did VS against ZINC8 using 3kys as protein model, and selected top 100000 2nd round: The did VS using 5 representative MD snapshots of 3kys, and selected 1000 hits

    2. The selection process from 1000 (seeSupplement Data File S1) to thefinal list of 16 compounds

      3rd VS: visual inspection and property filter

    3. he enrichment process from thefirst BUDEdocking reduced the number of conformers from 160 millionto 100 000

      1st VS: 100000 hits


    1. Timings for Open3DALIGN validation suites

      speed is provided. thanks to the author

    2. (0.02 s conformation-1)

      2 seconds for 100 alignment.

    3. themixed and atom-based superposition algorithms are thosegiving rise to the most consistent and well-ordered align-ments,

      atom-based and mixed algorithms are recommended.



    1. 0.6mgof recombinant AR, SRC-3 and p300 proteins were incubated with 200 ng of ARE DNA in the presence of 1mM R1881

      the SRC-3 and p300 should be full length protein

    2. AR interacts with SRC-3 through its N-terminal domain (NTD)

      this is contradictory with previous observation that LBD binds with SRC3. https://www.jbc.org/content/early/2010/01/19/jbc.M109.085779.full.pdf?with-ds=yes However, previous result are based on only the truncated AR with SRC3 peptide, which is far from the native state of full length AR and SRC. So I trust the current finding.

    3. AR Recruits SRC-3 and p300 Mainly through Its NTD

      this is contradictory with previous observation that LBD binds with SRC3. https://www.jbc.org/content/early/2010/01/19/jbc.M109.085779.full.pdf?with-ds=yes However, previous result are based on only the truncated AR with SRC3 peptide, which is far from the native state of full length AR and SRC. So I trust the current finding.

    4. Preclinical studies of a p300 inhib-itor also reveal efficacy in patient-derived prostate tumor ex-plants (Butler et al., 2019) and the growth of castration-resistantprostate cancer (Jin et al., 2017)


      would p300 inhibitor be more effective to prostate cancer than AR inhibitor? would p300 inhibitor have more off-target issues?

    5. this is a Cryo-EM paper. It demonstrated how scientist map proteins to the volume data from EM. The author combined result from antibody labelling, protein docking, pull down and CoIP to map the protein to the volume data.

    6. The rela-tively large-sized AR NTDs, however, wrap around the LBDs,blocking the access of SRC-3 to the LBD. Consequently,SRC-3 is solely recruited by the AR NTD, and p300 recruitmentis stabilized by contacting two AR NTDs

      AR NTD wrap around its LBD. Does AR NTD mimic the function of some NR co-activator? These conclusion is only true when AR agonist R1881 is added, check figure 4

    7. in the presence of 1mM R1881

      does AR NTD interact with SRC-3 without R1881?

    8. Based on the structure (Figure 3C), we did not observe thatSRC-3 directly contacts the AR LBDs. The interaction betweenSRC-3 and the AR NTD is clearly observed in our structuraldata

      SRC3 interacts with NTD, but not LBD as revealed by the structure

    9. both NTDs also connect toeach other to contribute to AR dimerization

      NTD forms PPI too

    10. The combination of the anti-body locations, crystal structure docking, and the observed DNA

      docking, antibody labelling and DNA position allows the modeling building



    1. different conformation of the β-helix region creates a hydrophobic cavity that is absent in tau filaments from the brains of patients with Alzheimer’s disease

      this cavity is a mystery revealed by this article. the authors believe it is a hydrophobic cavity. Actually, at similar position of the Alzheimer's tau filament, a smaller tunnel exists. beta-helix may mean a helical ultrastructure formed by beta sheet.

    2. astigmatism


    3. additional density—which is not present in the Alzheimer fold—is surrounded by the density of the tau protein chain within the ordered cor

      unrevealed density

    4. a predominant helical filament type in all three case

      helical filament is an assembly of tau protein


    1. FROG2

      it did not update since 2010.


    1. nscm

      nscm definition

    2. Low-MODe (LMOD) optimization methods

      Could this be used to LMW?

    3. LMOD

      could I use this for conformational search

    4. parm

      multiple topology files

    5. strip


    6. Coordinates (COORDS) Data Set Commands

      modify the trajectory immediately

    7. cluster


    8. cluster

      cluster the trajectory

    9. nscm

      nscm=0 by default, and 0 means no change is made to recenter the system This is used in Dan's WatMD production run, maybe because he put position restraints to the sytem, so he does not want Amber to recenter the system. http://archive.ambermd.org/200704/0199.html

    10. ntwr


    11. ntt




    1. icrosecond time scale molecular dynamics

      us scale MD

    2. How to deal with solute concentration in MD simulation?



    1. 11

      this paper may contain a dataset of kinetics