Jacob Verburgt
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Explore the profile of Jacob Verburgt including associated specialties, affiliations and a list of published articles.
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11
Citations
155
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Recent Articles
1.
Lawson C, Kryshtafovych A, Pintilie G, Burley S, cerny J, Chen V, et al.
Nat Methods
. 2024 Jun;
21(7):1340-1348.
PMID: 38918604
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at...
2.
Lawson C, Kryshtafovych A, Pintilie G, Burley S, cerny J, Chen V, et al.
Res Sq
. 2024 Feb;
PMID: 38343795
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic...
3.
Zhang Z, Verburgt J, Kagaya Y, Christoffer C, Kihara D
bioRxiv
. 2023 Dec;
PMID: 38106114
Protein-peptide interactions play a key role in biological processes. Understanding the interactions that occur within a receptor-peptide complex can help in discovering and altering their biological functions. Various computational methods...
4.
Verburgt J, Jain A, Kihara D
Methods Mol Biol
. 2023 Sep;
2714:215-234.
PMID: 37676602
Identification and optimization of small molecules that bind to and modulate protein function is a crucial step in the early stages of drug development. For decades, this process has benefitted...
5.
Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, et al.
Proteomics
. 2023 Jun;
23(17):e2200323.
PMID: 37365936
Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to...
6.
Verburgt J, Zhang Z, Kihara D
Methods
. 2022 May;
204:55-63.
PMID: 35609776
Intrinsically Disordered Proteins (IDPs) are a class of proteins in which at least some region of the protein does not possess any stable structure in solution in the physiological condition...
7.
Rao R, Ahsan N, Xu C, Su L, Verburgt J, Fornelli L, et al.
Evol Bioinform Online
. 2021 Dec;
17:11769343211064616.
PMID: 34898980
SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 5.0 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants...
8.
Lensink M, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil R, et al.
Proteins
. 2021 Aug;
89(12):1800-1823.
PMID: 34453465
We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and...
9.
Verburgt J, Kihara D
Proteins
. 2021 Jul;
90(1):83-95.
PMID: 34309909
Protein structure docking is the process in which the quaternary structure of a protein complex is predicted from individual tertiary structures of the protein subunits. Protein docking is typically performed...
10.
Christoffer C, Terashi G, Shin W, Aderinwale T, Maddhuri Venkata Subramaniya S, Peterson L, et al.
Proteins
. 2019 Nov;
88(8):948-961.
PMID: 31697428
We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI) rounds 38-46. The pipeline integrates programs...