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References from Computer aided drug design in the development of proteolysis targeting chimeras. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1073/pnas.141230798
10.1073/pnas.141230798 · External reference
10.1038/s41573-021-00371-6
10.1038/s41573-021-00371-6 · External reference
PROTAC technology: opportunities and challenges
10.1021/acsmedchemlett.9b00597 · 2020 · External reference
Current strategies for the design of PROTAC linkers: a critical review
10.37349/etat.2020.00018 · 2020 · External reference
10.1021/acsptsci.1c00118
10.1021/acsptsci.1c00118 · External reference
10.1038/s41586-019-0917-9
10.1038/s41586-019-0917-9 · External reference
10.1021/acscentsci.7b00512
10.1021/acscentsci.7b00512 · External reference
10.1021/acs.jcim.8b00537
10.1021/acs.jcim.8b00537 · External reference
Unresolved reference
External reference
PROTAC-DB 2.0: an updated database of PROTACs
2022 · External reference
10.1021/acs.jcim.8b00839
10.1021/acs.jcim.8b00839 · External reference
10.1021/acs.jcim.9b01120
10.1021/acs.jcim.9b01120 · External reference
Unresolved reference
2020 · External reference
10.1038/s42256-022-00527-y
10.1038/s42256-022-00527-y · External reference
10.26434/chemrxiv-2022-qkx9f
10.26434/chemrxiv-2022-qkx9f · External reference
10.1021/acs.jcim.0c00915
10.1021/acs.jcim.0c00915 · External reference
Unresolved reference
External reference
10.1021/acs.jcim.2c00838
10.1021/acs.jcim.2c00838 · External reference
10.26434/chemrxiv.12843137.v1
10.26434/chemrxiv.12843137.v1 · External reference
10.1016/s0169-409x(00)00129-0
10.1016/s0169-409x(00)00129-0 · External reference
How beyond rule of 5 drugs and clinical candidates bind to their targets
2016 · External reference
10.1016/j.chembiol.2014.08.013
10.1016/j.chembiol.2014.08.013 · External reference
10.1021/acs.jmedchem.8b01732
10.1021/acs.jmedchem.8b01732 · External reference
Computational prediction of formulation strategies for beyond-rule-of-5 compounds
10.1016/j.addr.2016.02.005 · 2016 · External reference
10.1016/j.drudis.2020.03.012
10.1016/j.drudis.2020.03.012 · External reference
Optimising proteolysis-targeting chimeras (PROTACs) for oral drug delivery: a drug metabolism and pharmacokinetics perspective
10.1016/j.drudis.2020.07.013 · 2020 · External reference
Designing soluble PROTACs: strategies and preliminary guidelines
10.1021/acs.jmedchem.2c00201 · 2022 · External reference
Impact of dynamically exposed polarity on permeability and solubility of chameleonic drugs beyond the rule of 5
10.1021/acs.jmedchem.8b00347 · 2018 · External reference
Poorly soluble marketed drugs display solvation limited solubility
10.1021/jm0706416 · 2007 · External reference
Hybrid alchemical free energy/machine-learning methodology for the computation of hydration free energies
10.1021/acs.jcim.0c00600 · 2020 · External reference
How big is too big for cell permeability?
10.1021/acs.jmedchem.7b00237 · 2017 · External reference
10.1021/acs.jmedchem.6b01483
10.1021/acs.jmedchem.6b01483 · External reference
Predicting the permeability of macrocycles from conformational sampling – limitations of molecular flexibility
10.1016/j.xphs.2020.10.052 · 2021 · External reference
Linker-dependent folding rationalizes PROTAC cell permeability
10.1021/acs.jmedchem.2c00877 · 2022 · External reference
10.26434/chemrxiv-2022-jmx90
10.26434/chemrxiv-2022-jmx90 · External reference
10.1021/acs.jcim.0c00280
10.1021/acs.jcim.0c00280 · External reference
Fast estimation of the blood–brain barrier permeability by pulling a ligand through a lipid membrane
10.1021/acs.jcim.9b00834 · 2020 · External reference
10.1021/acs.jcim.8b00872
10.1021/acs.jcim.8b00872 · External reference
Unresolved reference
External reference
ProsetTac: rosetta based modeling of PROTAC mediated ternary complexes
10.1021/acs.jcim.0c00589 · 2020 · External reference
Shape change in crystallization of biological macromolecules
10.1557/mrs.2016.87 · 2016 · External reference
10.1021/acs.jmedchem.1c01576
10.1021/acs.jmedchem.1c01576 · External reference
10.1101/2022.06.03.494737
10.1101/2022.06.03.494737 · External reference
10.4155/fmc-2017-0261
10.4155/fmc-2017-0261 · External reference
Inclusion of desolvation energy into protein–protein docking through atomic contact potentials
10.1021/acs.jcim.1c01483 · 2022 · External reference
CLUB-MARTINI: selecting favourable interactions amongst available candidates, a coarse-grained simulation approach to scoring docking decoys
10.1371/journal.pone.0155251 · 2016 · External reference
Protein-protein docking refinement using restraint molecular dynamics simulations
2016 · External reference
Assessment of ab initio models of protein complexes by molecular dynamics
10.1371/journal.pcbi.1006182 · 2018 · External reference
Refining evERdock: improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations
10.1063/1.5055799 · 2018 · External reference
Evaluation of predicted protein-protein complexes by binding free energy simulations
10.1021/acs.jctc.8b01022 · 2019 · External reference
Prediction of protein–protein complexes using replica exchange with repulsive scaling
10.1002/jcc.26187 · 2020 · External reference
Efficient refinement and free energy scoring of predicted protein–protein complexes using replica exchange with repulsive scaling
10.1021/acs.jcim.0c00853 · 2020 · External reference
Enhanced molecular dynamics method to efficiently increase the discrimination capability of computational protein–protein docking
10.1021/acs.jctc.1c00789 · 2021 · External reference
10.1021/ja026939x
10.1021/ja026939x · External reference
Improved modeling of peptide-protein binding through global docking and accelerated molecular dynamics simulations
10.3389/fmolb.2019.00112 · 2019 · External reference
GroScore: accurate scoring of protein–protein binding poses using explicit-solvent free-energy calculations
10.1021/acs.jcim.9b00687 · 2019 · External reference
10.1021/acs.jmedchem.1c02155
10.1021/acs.jmedchem.1c02155 · External reference
10.1038/nprot.2016.169
10.1038/nprot.2016.169 · External reference
Protein docking model evaluation by graph
2021 · External reference
Native or non-native protein-protein docking models? Molecular dynamics to the rescue
10.1021/acs.jctc.1c00336 · 2021 · External reference
Computational prediction of protein–protein binding affinities
10.1002/wcms.1448 · 2020 · External reference
10.1529/biophysj.108.131383
10.1529/biophysj.108.131383 · External reference
10.1021/ct400273t
10.1021/ct400273t · External reference
Computing protein-protein association affinity with hybrid steered molecular dynamics
10.1021/acs.jctc.5b00340 · 2015 · External reference
10.1073/pnas.1815431116
10.1073/pnas.1815431116 · External reference
Simulation of reversible protein–protein binding and calculation of binding free energies using perturbed distance restraints
10.1021/acs.jctc.7b00706 · 2017 · External reference
Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
10.1038/s41467-017-01163-6 · 2017 · External reference
10.1038/nchem.2785
10.1038/nchem.2785 · External reference
Quantifying protein–protein interactions in molecular simulations
10.1021/acs.jpcb.9b11802 · 2020 · External reference
Protein–protein interaction-gaussian accelerated molecular dynamics (PPI-GaMD): characterization of protein binding thermodynamics and kinetics
10.1021/acs.jctc.1c00974 · 2022 · External reference
DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs
10.1038/s41467-022-34807-3 · 2022 · External reference
10.1016/j.jbc.2022.101653
10.1016/j.jbc.2022.101653 · External reference
10.1016/j.sbi.2020.10.009
10.1016/j.sbi.2020.10.009 · External reference
10.1021/acs.jcim.0c00897
10.1021/acs.jcim.0c00897 · External reference
