- Dec 2020
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frontiermeds.com frontiermeds.com
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an expert in fragment-based and covalent drug discovery.
FBDD expert
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Chief Scientific Officer of Arvinas
a senior industry leader
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Johannes holds a Ph.D. in quantum & molecular mechanics
he is a CADD Ph. D
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data science expert
data science expert
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global Head for Data Science at Johnson & Johnson Medical Devices Technology
a senior industry leader
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Vice President of Oncology Research at AstraZeneca
Kevin is a senior industry leader
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DANIEL K. NOMURA, Ph.D.
Nomura is collaborting with Novartis to identify covalent binders. Novartis provide CADD and chemical library
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- Nov 2020
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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by attaching acceptor and donor to different domains of a target protein, the interdomain dynamics can be monitored
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www.scripps.edu www.scripps.edu
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Journal of the American Chemical Society. 2018, 140, 8069-8073.
covalent warhead
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URL
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- Oct 2020
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rdkit.blogspot.com rdkit.blogspot.com
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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
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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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.
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www.sciencedirect.com www.sciencedirect.com
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30-min pre-incubation of inhibitors and BTK
pre-incubation time is 30 min
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- Aug 2020
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publications.iupac.org publications.iupac.org
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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
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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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?
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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.
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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
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Local file Local file
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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
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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
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Thecovalentinhibitordisplayeda5-foldincreasein cellularactivitycomparedto the reversiblecounterpart
cellular activity improvement
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To stabilizethe readilyreversiblealdimineadduct,anortho-boronicacidgroupwas included
aldehyde forms reversible adduct with lysine. attention
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5MKS
the covalent bond is missing in the release structure.
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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.
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N-a-acetyl-lysine
CC(=O)NC@@HC(O)=O
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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
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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
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NOE-Based Methods
STD is one of the NOE based methods
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NMR in SBDD review
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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
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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.
amplified
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This is in agreementwiththe lackof slowlyexchangingpolarresiduesin the CTBbindingpocket
So D2O/H2O differential STD will highlight the slow exchange polar protein H
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use of solventsuppression
How to do this?
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aromaticproteinspectralregions
if compound contains aryl ring, this frequency should not be used to saturate the system, then how should we choose this frequency?
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theseproton
proton of polar residues
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Anothersourceof minordifferencesinepitopemapsisthesolven
Hydrogen atoms of polar residues will be exchanged to Deuterium when solvent is D2O. In contrast, they will not excha
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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.
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onlinelibrary.wiley.com onlinelibrary.wiley.com
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x 64
what does this mean? count of detections?
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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.
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Y525, which is known to have a very fast kinetics of exchange
this is measured previously
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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
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protonated residues within 4 Å
4 A?
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100%D2O
100% D2O is needed, to allow sufficient STD to ligand and not water or other solvent.
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SaturationtransferNMRwasapioneeringtechniquedevelopedin1979
STD was used first in 1979
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wereobtainedbycollecting128scans
number of scans can be accumulated?
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nfact,thereisanincreaseofsensitivitywiththesizeofproteinduetoamoreefficientinter-andintramolecularsaturationtransfer
larger size of protein will increase the sensitivity due to more efficient inter- and intramolecular saturation transfer
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Usinghigherfieldspectrometerswillmakethemethodevenmoreefficientsincesensitivityandspindiffusionincreasewithfieldstrength
higher field strength will help increase the sensitivity
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wheatgermagglutinin
212 amino acids https://www.uniprot.org/uniprot/P10968
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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
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highturnoverratesresultinalargereffectathigherligand-to-proteinratios.SlowdissociationrateswillyieldsmallerSTDNMRsignalsand,thus,reducesensitivity
Slow dissociation rates will yield smaller STD NMR signals and, thus, reduce sensitivity
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www2.chem.wisc.edu www2.chem.wisc.edu
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NMR STD experiment
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The on-resonance frequency needs to be optimized for each protein
How to optimize it? How to measure if the frequency is good enough?
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excess concentration of ligand
EL hereafter
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www.rsc.org www.rsc.org
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Off‐ratescreening
Off‐rate screening
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Thermalmeltmethodsunreliable
I agree
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nn8
number of entries on line
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Substitution Count [Query]
substitution count
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- Jul 2020
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restrictingligandconformationalflexibilityacceleratedthebinding
conformation is related to kon
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seriesofagonistsoftheA2Aadenosinereceptor
really? I need to check the original data.
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narrowpassageway
How to define is a passageway is narrow or not?
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diffusion-limitedon-rate(kon109M1s1)
this should be the maximum kon, right?
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the key method for conformation comparison used in this artical is wrong, so the result is not very informative.
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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?
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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
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AMBERTOOLS14[59] adopting GAFFparameters [42] for the molecule and the TIP3P model of water
GAFF for LMW, TIP3P water
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GAUSSIAN09
commercial QM tool
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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
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(i) consistent with that obtained from REMD simulations
plain MD sampled similar conformational space as REMD How they measured?
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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
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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
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The selection process from 1000 (seeSupplement Data File S1) to thefinal list of 16 compounds
3rd VS: visual inspection and property filter
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he enrichment process from thefirst BUDEdocking reduced the number of conformers from 160 millionto 100 000
1st VS: 100000 hits
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Timings for Open3DALIGN validation suites
speed is provided. thanks to the author
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(0.02 s conformation-1)
2 seconds for 100 alignment.
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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.
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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
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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.
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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.
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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)
https://ascopubs.org/doi/abs/10.1200/JCO.2019.37.15_suppl.e16534
would p300 inhibitor be more effective to prostate cancer than AR inhibitor? would p300 inhibitor have more off-target issues?
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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.
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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
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in the presence of 1mM R1881
does AR NTD interact with SRC-3 without R1881?
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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
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both NTDs also connect toeach other to contribute to AR dimerization
NTD forms PPI too
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The combination of the anti-body locations, crystal structure docking, and the observed DNA
docking, antibody labelling and DNA position allows the modeling building
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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.
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astigmatism
像散
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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
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a predominant helical filament type in all three case
helical filament is an assembly of tau protein
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Local file Local file
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FROG2
it did not update since 2010.
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Local file Local fileAmber20.pdf22
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nscm
nscm definition
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Low-MODe (LMOD) optimization methods
Could this be used to LMW?
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LMOD
could I use this for conformational search
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parm
multiple topology files
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strip
strip
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Coordinates (COORDS) Data Set Commands
modify the trajectory immediately
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cluster
cluster
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cluster
cluster the trajectory
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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
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ntwr
ntwr
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ntt
ntt
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tempi
tempi
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temp0
temp0
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ntr
ntr
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ntc
ntc
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taup
taup
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igb
igb
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ig
ig
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irest
irest
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imin
imin
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rms | rmsd
rms
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Atom Mask Selection Syntax
selection syntax
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Local file Local file
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11
this paper may contain a dataset of kinetics
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Local file Local file
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KI-MS2-002
structure of KI-MS2-002
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Local file Local file
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The F2X-Entry Screen is a subset of the F2X-Universal Library
F2X entry is a subset of F2X universal
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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
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the PanDDA approachincreased the hit yield significantl
PanDDA method seems good
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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
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FragMAXapp
https://www.maxiv.lu.se/industry/ it is a synchrotron facility
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numerous commercial libraries are availableon the market, a large subset of them being reviewed in detail
need to read this paper
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- Jun 2020
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practicalfragments.blogspot.com practicalfragments.blogspot.com
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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
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Soaking each of the compounds at 100 mM yielded 8 structures, 5 of which bound in the active site.
100mM soaking of each compound
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crystallography has become the most popular technique for FBLD
FBDD by crystallography is most popular from 2019
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cryoprotectant
防冻剂
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Local file Local file
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Local file Local file
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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
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00 μmol/L of the compound mixture
working solution of mixture NMR: 200 uM compound, 20 uM protein
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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?
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Chemdiv and Enamine,
vendors
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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
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emphasizing X-ray crystallography.
emphasizing X-ray is Astex's way
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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.
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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.
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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?
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observe a correlation of 30–40% using these two techniques.
only 30~40% correlation between X-ray and ligand observed NMR
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use ligand-observed NMR
Does "ligand observed NMR" equal to "ligand 1D-NMR"
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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.
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that current fragment libraries are largely composed of ‘flat structures’
flat structures are not good enough for some protein targest?
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our results support the view that less complex molecules give a higher hit rat
FBDD is good for hit identification
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practicalfragments.blogspot.com practicalfragments.blogspot.com
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cryoprotectant
防冻剂
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bits.csb.pitt.edu bits.csb.pitt.edu
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TIGIT small molecule allosteric inhibitor
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but subsequent trials failed to show any acti
cellular activity is not promising
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cadd cadd
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UT-34 induced the regression of enzalutamide-resistant tumors at doses when the AR is degraded
What dose?
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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
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Local file Local file
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Local file Local file
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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?
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more than5000 different compounds have been isolated fromabout 500 species of sponges
will this reference provide a list of extracts of marine sponges
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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
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Dynamic properties of PPAR-γ
molecule is intrisincly dynamic
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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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
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he studies using the LNCaP xenograft tumor model show that JJ-450 can suppress AR functionin vivo
in vivo activity
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inhibiting both full-length AR andAR splice variants lacking LBD.
inhibit both FL and ARv7
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with ()-JJ-450 beingapproximately 9-fold more potent than (þ)-JJ-450 in the luciferasePSA-reporter assay (24)
chirality is important for the activity
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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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
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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
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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)
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Local file Local file
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. 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.
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- May 2020
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Local file Local file
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6TX6, 6TX4, 6TX7, 6TX8, 6TX5 and 6TX9). (
crystal structures solved in this paper
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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
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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
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site-identification by ligand competitive saturation (SILCS)
SILCS
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MiniFrags
crystallograpy method for hit finding
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Local file Local file
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IkBaphosphopeptide (IPP)
peptide binder to beta-TRCP
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Local file Local file
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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
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10.2 inclusive
CUDA10.2 is supported
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ecommended choice isgaff2
gaff2 is recommended for organic molecule
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gamma_ln
collision frequency, in ps-1
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OPCwater model in combination with the ff99SB was found to improve, significantly, accuracy of atomistic simulationsof IDPs
Myc is a typical IDP. To model Myc, force field must be carefully chosen.
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ff19SB
ff19SB
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ambermd.org ambermd.org
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wt1mg_min_water
should be wt1mg_min.rst
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Local file Local file
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ecommended choice isgaff2
gaff2 is recommended for organic compounds
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nrt1 deletion
highlights one transporter thatdisplays a significant extent of such resistance (as thenrt1dele-tant).NRT1encodes a nicotinamide riboside transporter, whichled us to hypothesize (i) that such a deletant would display resis-tance to DPI when cultured axenically, and (ii) that nicotinic acidwould be able to compete with the DPI and effect phenotypicresistance.Figure 2Bshows that both predictions are entirelyfulfilled
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DPI
Diphenylene iodonium
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ramifications
后果
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Protein:lipid~3:1
this ratio is contrary to the quote 1:10 Lipitor get through the membrane through OATP1B1?
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sapiens
Human cell has the most number of carriers
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Over 60 Drug Discovery Webinars
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cbio.bmt.tue.nl cbio.bmt.tue.nl
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This is a good overview of the common potentials of a force field
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ambermd.org ambermd.org
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4 missing angle parameters
no missing angle parameters when processed in Amber18
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Ideally you should really test these parameters (by comparing to ab initio calculations for example) to ensure they are reasonable
How to compare?
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parmchk
parmchk2 in Amber18
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C, N, O, S, P, H, F, Cl, Br and I
GAFF only supports 10 elements?
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GAFF
GAFF
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Annotators
URL
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the commented Python scripts optFromSmiles.py, optLigandInProtein.py and torsionalScan.py which serve as examplesof simple and constrained MMFF minimizations
I will learn these scripts
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ositionalCartesian restraint
Cartesian restraints are available in Schrodinger MacroModel, how to implement them? some example scripts are included in Additional file 1 of this article
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The possibility of adding these restrainingpotentials to the force field expression has also beenadded to the existing RDKit UFF implementation
Rdkit UFF also support cartesian restraints
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relax ligand-receptor complexeswithout causing major alterations of their originalgeometry, or to perform a torsional scan on a selecteddihedral while relaxing the rest of the molecule.
such functions are like Schrodinger MacroModel, how to implement them?
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www.sciencedirect.com www.sciencedirect.com
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SARS-CoV PLpro
SARS-CoV PLpro PDB, 2fe8
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www.sciencedirect.com www.sciencedirect.com
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MONN contains a pairwise interaction prediction module, which can capture the non-covalent interactions between atoms of a compound and residues of a protein with extra supervision from the labels extracted from available high-quality 3D compound-protein complex structures
does that mean MONN can predict binding site
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this is done by Tshinghua Univ
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- Apr 2020
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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this seems to be a review
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Arv7
ARv7
Tags
Annotators
URL
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vina.scripps.edu vina.scripps.edu
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AutoDock Vina ignores the user-supplied partial charges
partial charge is ignored because the scoring function treated electrostatic interactions with other parameters.
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pubs.acs.org pubs.acs.org
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available
commercialized?
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