Co-folding model guided by structural proteomics | Paper Citation Record

Observation 1d8bc285-35dc-4f12-97e8-4a88839d2b36 · outbound

This paper cites PROTAC targeted protein degraders: the past is prologue.Nat Rev Drug Discov, 21(3):181–200, March 2022.

Co-folding model guided by structural proteomics PROTAC targeted protein degraders: the past is prologue.Nat Rev Drug Discov, 21(3):181–200, March 2022

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Observation d50f8c30-4880-4947-84a9-7c761545f739 · outbound

This paper cites The rise of molecular glues.Cell, 184(1):3–9, January 2021.

Co-folding model guided by structural proteomics The rise of molecular glues.Cell, 184(1):3–9, January 2021

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Co-folding model guided by structural proteomics Unresolved cited work

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This paper cites Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation.Nat.

Co-folding model guided by structural proteomics Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation.Nat

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This paper cites Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.RSC Chem.

Co-folding model guided by structural proteomics Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.RSC Chem

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This paper cites Molecular recognition of ternary complexes: a new dimen- sion in the structure-guided design of chemical degraders.Essays Biochem., 61(5):505–516, November 2017.

Co-folding model guided by structural proteomics Molecular recognition of ternary complexes: a new dimen- sion in the structure-guided design of chemical degraders.Essays Biochem., 61(5):505–516, November 2017

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Co-folding model guided by structural proteomics High accuracy prediction of PROTAC complex structures.J

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This paper cites Plasticity in binding confers selectivity in ligand-induced protein degradation.Nat Chem Biol, 14(7): 706–714, July 2018.

Co-folding model guided by structural proteomics Plasticity in binding confers selectivity in ligand-induced protein degradation.Nat Chem Biol, 14(7): 706–714, July 2018

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This paper cites Development of targeted protein degradation therapeutics.Nat Chem Biol, 15(10):937–944, October 2019.

Co-folding model guided by structural proteomics Development of targeted protein degradation therapeutics.Nat Chem Biol, 15(10):937–944, October 2019

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Observation a8a203bb-1132-4e73-8aed-cf7f4c7dea46 · outbound

This paper cites Accurate structure prediction of biomolecular interactions with AlphaFold 3.

Co-folding model guided by structural proteomics Accurate structure prediction of biomolecular interactions with AlphaFold 3

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Observation 348ce52d-cbcd-445a-b09e-2f584d5ec283 · outbound

This paper cites Boltz-2: Towards accurate and efficient binding affinity prediction.

Co-folding model guided by structural proteomics Boltz-2: Towards accurate and efficient binding affinity prediction

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Observation ba126190-49e9-4728-9cf5-74182811b8aa · outbound

This paper cites Har- nessing AlphaFold to reveal hERG channel conformational state secrets.Elife, 13(RP104901): RP104901, July 2025.

Co-folding model guided by structural proteomics Har- nessing AlphaFold to reveal hERG channel conformational state secrets.Elife, 13(RP104901): RP104901, July 2025

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Observation 2c6dec03-e7a6-47f6-8fdd-6f77f91306dd · outbound

This paper cites Protein structure prediction has reached the single-structure frontier.Nat Methods, 20(2):170–173, February 2023.

Co-folding model guided by structural proteomics Protein structure prediction has reached the single-structure frontier.Nat Methods, 20(2):170–173, February 2023

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Observation 03fdc07f-3225-42a1-ba99-385b65b95502 · outbound

This paper cites Challenges in predicting PROTAC-mediated protein-protein interfaces with AlphaFold reveal a general limitation on small interfaces.Bioinform.

Co-folding model guided by structural proteomics Challenges in predicting PROTAC-mediated protein-protein interfaces with AlphaFold reveal a general limitation on small interfaces.Bioinform

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Observation 254d2917-1dc5-4bcc-b28a-ee165168df3a · outbound

This paper cites Predicting PROTAC- mediated ternary complexes with AlphaFold3 and boltz-1.Digit.

Co-folding model guided by structural proteomics Predicting PROTAC- mediated ternary complexes with AlphaFold3 and boltz-1.Digit

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Observation 2ff622f0-b6c4-4315-ba2e-e72db87a2460 · outbound

This paper cites Cross-linking mass spectrometry for mapping protein complex topologies in situ.Essays Biochem, 67(2):215–228, March 2023.

Co-folding model guided by structural proteomics Cross-linking mass spectrometry for mapping protein complex topologies in situ.Essays Biochem, 67(2):215–228, March 2023

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Observation cbefa9ed-f37d-4e1b-90d9-5fe1b48b5680 · outbound

This paper cites Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.Nat Methods, 16(7):595–602, July 2019.

Co-folding model guided by structural proteomics Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.Nat Methods, 16(7):595–602, July 2019

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Observation d0f4115e-9078-4620-8ce8-d5787d87f1cf · outbound

This paper cites Extrapolating foundation generative models with physics: A case study of exploring peptide conformations under protein-environment interactions.J.

Co-folding model guided by structural proteomics Extrapolating foundation generative models with physics: A case study of exploring peptide conformations under protein-environment interactions.J

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Co-folding model guided by structural proteomics HDXRank: A deep learning framework for ranking protein complex predictions with hydrogen-deuterium exchange data.J

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Co-folding model guided by structural proteomics RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data.J

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Co-folding model guided by structural proteomics DOT2: Macromolecular docking with improved biophysical models.J

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Co-folding model guided by structural proteomics Diffusion posterior sampling for general noisy inverse problems

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Co-folding model guided by structural proteomics Score-based generative modeling through stochastic differential equations

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Co-folding model guided by structural proteomics Reverse-time diffusion equation models.Stoch

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Co-folding model guided by structural proteomics A connection between score matching and denoising autoencoders.Neural Comput, 23(7):1661–1674, July 2011

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Co-folding model guided by structural proteomics Tweedie’s formula and selection bias.J Am Stat Assoc, 106(496):1602–1614, 2011

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Observation 67e2de49-b77a-4503-afdf-6d58ca1ba91a · outbound

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Co-folding model guided by structural proteomics Hydrogen deuterium exchange defines catalytically linked regions of protein flexibility in the catechol o-methyltransferase reaction.Proc

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Co-folding model guided by structural proteomics HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.J Am Chem Soc, 125(7): 1731–1737, February 2003

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Co-folding model guided by structural proteomics Principles for integrative structural biology studies.Cell, 177 (6):1384–1403, May 2019

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Co-folding model guided by structural proteomics Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning.Nat Biotechnol, 41(12):1810–1819, December 2023

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Co-folding model guided by structural proteomics Modelling protein complexes with crosslinking mass spectrometry and deep learning.Nat Commun, 15(1):7866, September 2024

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Co-folding model guided by structural proteomics Multiscale guidance of protein structure prediction with heterogeneous cryo-EM data

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Co-folding model guided by structural proteomics DockQ: A quality measure for Protein-Protein docking models

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Co-folding model guided by structural proteomics Maximum allowed solvent accessibilites of residues in proteins.PLoS One, 8(11): e80635, November 2013

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Co-folding model guided by structural proteomics Design of a cereblon construct for crystallo- graphic and biophysical studies of protein degraders.Nature Communications, 15(1):8885, October 2024

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Co-folding model guided by structural proteomics Crystal structures of DCAF1-PROTAC-WDR5 ternary complexes provide insight into DCAF1 substrate specificity.Nat Commun, 15(1):10165, November 2024

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Co-folding model guided by structural proteomics Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex.Commun Chem, 7(1):183, August 2024

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Co-folding model guided by structural proteomics Impact of protein conformational diversity on AlphaFold predictions.Bioinformatics, 38(10):2742–2748, April 2022

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Co-folding model guided by structural proteomics Structural basis of PROTAC cooperative recognition for selective protein degradation.Nat Chem Biol, 13(5):514–521, May 2017

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Co-folding model guided by structural proteomics In silico modeling of PROTAC-Mediated ternary complexes: Validation and application.J Chem Inf Model, 59(4):1634–1644, April 2019

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Co-folding model guided by structural proteomics Comprehensive evaluation of fourteen docking programs on Protein-Peptide complexes.J Chem Theory Comput, 16(6):3959–3969, June 2020

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Co-folding model guided by structural proteomics Ultrafiltration-enhanced cross-linking mass spectrometry for comprehensive analysis of low molecular weight protein cross-links.Anal

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Co-folding model guided by structural proteomics HRaDeX: R package and web server for computing high-resolution deuterium uptake rates for HDX-MS data.J

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