329 Matching Annotations
  1. 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

  2. Jun 2021
  3. 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

  4. Apr 2021
  5. 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

  6. 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

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

      covalent warhead

  8. 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.

  9. 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. NMR STD experiment

    2. The on-resonance frequency needs to be optimized for each protein

      How to optimize it? How to measure if the frequency is good enough?

    3. excess concentration of ligand

      EL hereafter

    1. nn8

      number of entries on line

    2. Substitution Count [Query]

      substitution count


  10. 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?

    8. there is a negligible impact of these differences on zwitterionicAMP dynamics as sampled alongμs-long MD simulations using both sets of charges

      charges did not show significant difference for MD



    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


    12. tempi


    13. temp0


    14. ntr


    15. ntc


    16. taup


    17. igb


    18. ig


    19. irest


    20. imin


    21. rms | rmsd


    22. Atom Mask Selection Syntax

      selection syntax



    1. icrosecond time scale molecular dynamics

      us scale MD

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

    3. Solvent-balance method of computing binding enthalpies.

      the total potential energy of each system is used ?



    1. 11

      this paper may contain a dataset of kinetics


    1. The F2X-Entry Screen is a subset of the F2X-Universal Library

      F2X entry is a subset of F2X universal

    2. However, for compound libraries witheven smaller compounds (about five to seven non-hydrogenatoms) higher hit rates were reported

      the smaller the fragment, the higher the hit rate. the purpose of different fragment libraries are different, both want to identify hot spots, and Reilly wanted to help MedChem optimization

    3. the PanDDA approachincreased the hit yield significantl

      PanDDA method seems good

    4. Of these, 10 hits (10 binding events) were observed onAar2, 11 hits (12 binding events) on RNaseH, and 1 hit (one bind-ing event) at the functional interface of the two proteins

      exciting results, 3 binding sites were identified with ligand

    5. FragMAXapp

      https://www.maxiv.lu.se/industry/ it is a synchrotron facility

    6. numerous commercial libraries are availableon the market, a large subset of them being reviewed in detail

      need to read this paper


  11. Jun 2020
    1. All of the fragment hits in this case were identified through visual inspection of the electron density maps

      manual inspection of the density map to find the binder

    2. Soaking each of the compounds at 100 mM yielded 8 structures, 5 of which bound in the active site.

      100mM soaking of each compound

    3. crystallography has become the most popular technique for FBLD

      FBDD by crystallography is most popular from 2019

    4. cryoprotectant


    1. 1,103-membered F2X-Universal Library

      what compounds are contained in the library?

    2. ry presentation of the libraries al-lows CFS campaigns to be carried out with or without the co-solvent DMSO present.

      what does "dry presentation" mean?



    1. 200 μmol/L potential hit compound or 200 μmol/L potential hit compound in the presence of 5 μmol/L protein.

      working solution of single compound NMR: 200 uM compound, 5 uM protein

    2. 00 μmol/L of the compound mixture

      working solution of mixture NMR: 200 uM compound, 20 uM protein

    3. DMSO-d6 stock solu-tions with a group compound concentration of 10 mmol/L were prepared and used for screening

      stock solution: 10 mM = sum of conc. of all group member?

    4. Chemdiv and Enamine,



    1. During the fragment hit-to-lead process, we typically synthesize 50–100 compounds to increase the binding affinity from millimolar to nanomolar, and we routinely generate multiple lead series for each target

      50-100 compounds from millimolar to nanomolar, that is too successful, 10^6 increase

    2. emphasizing X-ray crystallography.

      emphasizing X-ray is Astex's way

    3. the most potent fragment is often not the best starting point for hit-to-lead chemistry.

      a good lession: the most potent hit may not be the best starting point for further optimization.

    4. Although better cross-validation would provide increased confidence in fragment hits, there is a danger that this may also result in the systematic selection of more potent hits,

      this is a dilemma, if you expect a hit to be validated in both NMR and X-ray, you are actually expect a stronger binder.

    5. great importance should be placed on accurately characterizing the solubility of a fragment library

      for X-ray screening, solubility must be good enough. what is the cutoff?

    6. observe a correlation of 30–40% using these two techniques.

      only 30~40% correlation between X-ray and ligand observed NMR

    7. use ligand-observed NMR

      Does "ligand observed NMR" equal to "ligand 1D-NMR"

    8. Another area of active debate centres on the lack of correlation of fragment hits obtained using different detection techniques

      I have not notice this before, which reflects my lack of FBDD experiences.

    9. that current fragment libraries are largely composed of ‘flat structures’

      flat structures are not good enough for some protein targest?

    10. our results support the view that less complex molecules give a higher hit rat

      FBDD is good for hit identification



    1. TIGIT small molecule allosteric inhibitor

    2. but subsequent trials failed to show any acti

      cellular activity is not promising

    1. UT-34 induced the regression of enzalutamide-resistant tumors at doses when the AR is degraded

      What dose?

    2. T-34 caused the degradation of the full-length AR, but not the tau-5-deleted AR

      tau-5 locates between AF-1 and DBD, deletion of this region may cause significant protein structure change, such change may result in different AR degradation profile which is irrelavant with UT-34

    1. SDS-PAGE disrupts noncovalent interactions and is used to determine covalent binding.

      SDS-PAGE is used to identify covalent binder with the help of click chemistry



    1. chloroform extracts of ten marine sponges werescreened for their antimicrobial activit

      chloroform extracts were directly used without further separation for antimicrobial activity test. How to separate the active indigrient then?

    2. more than5000 different compounds have been isolated fromabout 500 species of sponges

      will this reference provide a list of extracts of marine sponges

    3. Since then well over 14,000 dif-ferent natural products from marine organismshave been described

      will this reference provide a list of extracts of marine sponges



    1. Our laboratory recently reported the structure of the intact PPARγ-RXRα heterodimer bound to its idealized DNA site, with coactivator peptides and ligands of both receptors

      the author of this review published the full length structure of PPARg

    1. he studies using the LNCaP xenograft tumor model show that JJ-450 can suppress AR functionin vivo

      in vivo activity

    2. inhibiting both full-length AR andAR splice variants lacking LBD.

      inhibit both FL and ARv7

    3. with ()-JJ-450 beingapproximately 9-fold more potent than (þ)-JJ-450 in the luciferasePSA-reporter assay (24)

      chirality is important for the activity



    1. Enzalutamide is an inhibitor of androgen-receptor signaling that exerts its activity by binding avidly to the ligand-binding domain of the androgen receptor, competing with and displacing the natural ligands of this receptor (testosterone and dihydrotestosterone)

      Enzalutamide binds to AR LBD

    1. A 2 fold molar excess of peptide was added to the protein prior to crystallization (RGAFQNLFQSV).

      why such a peptide is added for AR crystal structure?



    1. he discoveryof five distinct pockets in these complexes expands the possibilities fortargeting HIF protein activities with drug-like molecules for thera-peutic purposes.

      5 distinct pocket proposed in this paper

    2. A proposed mechanism by which 0X3 binding candestabilize the HIF-2a–ARNT heterodimer.

      R366 conformation is almost identical in apo and X03 bound structures(4zp4 vs 4zqd)


    1. . This mech-anistic hypothesis suggests perturbation of a few amino acidresidues within the PAS-B domain is sufficient to disrupt a largeprotein:protein interface leading to complete blockage of HIF2a-driven gene transcription

      in fact, the PPI is not disrupted, but altered.


  12. May 2020
    1. 6TX6, 6TX4, 6TX7, 6TX8, 6TX5 and 6TX9). (

      crystal structures solved in this paper

    2. ragment 1

      if fragment 1 is too acidic, then fragment 3 and 7 are too basic. And fragment 3 and 7 are not validated as binder

    3. this paper may related to the previous one of Daniel Seeliger. FBDD is not only useful for hit fidning, but also for MoA exploration. CADD is particular suitable for FBDD as the sampling of small molecule will more thourough

    4. site-identification by ligand competitive saturation (SILCS)


    5. MiniFrags

      crystallograpy method for hit finding



    1. IkBaphosphopeptide (IPP)

      peptide binder to beta-TRCP


    1. when using miniconda, you can’t move the Amber install folder fromits original location

      do not move amber install folder in bundled Miniconda is chosen during installation

    2. 10.2 inclusive

      CUDA10.2 is supported

    3. ecommended choice isgaff2

      gaff2 is recommended for organic molecule