Publications by authors named "Jacob Verburgt"

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Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning.
Yuki Kagaya, Tsukasa Nakamura, Jacob Verburgt, Anika Jain, Genki Terashi

Proteins· January 2026

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Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.
Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi, Jacob Verburgt

Proteins· January 2026

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Blind prediction of complex water and ion ensembles around RNA in CASP16.
Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi, Jacob Verburgt

bioRxiv· November 2025

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AlphaFold model quality self-assessment improvement via deep graph learning.
Jacob Verburgt, Zicong Zhang, Daisuke Kihara

Protein Sci· September 2025

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Learning with Privileged Knowledge Distillation for Improved Peptide-Protein Docking.
Zicong Zhang, Jacob Verburgt, Yuki Kagaya, Charles Christoffer, Daisuke Kihara

ACS Omega· July 2025

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Integrative Protein Assembly With LZerD and Deep Learning in CAPRI 47-55.
Charles Christoffer, Yuki Kagaya, Jacob Verburgt, Genki Terashi, Woong-Hee Shin

Proteins· March 2025

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Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiří Černý, Jacob Verburgt

Nat Methods· July 2024

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Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiří Černý, Jacob Verburgt

Res Sq· January 2024

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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.
Marc F Lensink, Guillaume Brysbaert, Nessim Raouraoua, Paul A Bates, Marco Giulini, Jacob C Verburgt

Proteins· December 2023

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Improved Peptide Docking with Privileged Knowledge Distillation using Deep Learning.
Zicong Zhang, Jacob Verburgt, Yuki Kagaya, Charles Christoffer, Daisuke Kihara

bioRxiv· December 2023

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Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.
Hugo Schweke, Qifang Xu, Gerardo Tauriello, Lorenzo Pantolini, Torsten Schwede, Jacob Verburgt

Proteomics· September 2023

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Recent Deep Learning Applications to Structure-Based Drug Design.
Jacob Verburgt, Anika Jain, Daisuke Kihara

Methods Mol Biol· September 2023

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Multi-level analysis of intrinsically disordered protein docking methods.
Jacob Verburgt, Zicong Zhang, Daisuke Kihara

Methods· August 2022

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Benchmarking of structure refinement methods for protein complex models.
Jacob Verburgt, Daisuke Kihara

Proteins· January 2022

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Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.
Marc F Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Jacob Verburgt

Proteins· December 2021

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Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein.
R Shyama Prasad Rao, Nagib Ahsan, Chunhui Xu, Lingtao Su, Jacob Verburgt

Evol Bioinform Online· December 2021

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Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches.
Nagib Ahsan, R Shyama Prasad Rao, Rashaun S Wilson, Ujwal Punyamurtula, Fernanda Salvato, Jacob C Verburgt

Proteomics· May 2021

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Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46.
Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Jacob Verburgt

Proteins· August 2020

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Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.
Jose L Olmos, Suraj Pandey, Jose M Martin-Garcia, George Calvey, Andrea Katz, Jacob Verburgt

BMC Biol· May 2018

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