Software package for simulations using the coarse-grained CALVADOS model

Authors: von Bülow, Sören, Yasuda, Ikki, Cao, Fan, Schulze, Thea K., Trolle, Anna Ida, Rauh, Arriën Symon, Crehuet, Ramon, Lindorff-Larsen, Kresten, Tesei, Giulio

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2504.10408

Machine learning methods to study sequence-ensemble-function relationships in disordered proteins

Authors: von Bülow, Sören, Tesei, Giulio, Lindorff-Larsen, Kresten

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2410.15940

Unwrapping NPT simulations to calculate diffusion coefficients

Authors: Bullerjahn, Jakob Tómas, von Bülow, Sören, Heidari, Maziar, Hénin, Jérôme, Hummer, Gerhard

Subject Terms: Physics - Computational Physics, Condensed Matter - Statistical Mechanics, Physics - Biological Physics

Access URL: http://arxiv.org/abs/2303.09418

Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries

Authors: Tsai, Yu-Xi, Chang, Ning-En, Reuter, Klaus, Chang, Hao-Ting, Yang, Tzu-Jing, von Bülow, Sören, Sehrawat, Vidhi, Zerrouki, Noémie, Tuffery, Matthieu, Gecht, Michael, Grothaus, Isabell Louise, Colombi Ciacchi, Lucio, Wang, Yong-Sheng, Hsu, Min-Feng, Khoo, Kay-Hooi, Hummer, Gerhard, Hsu, Shang-Te Danny, Hanus, Cyril, Sikora, Mateusz

Source: In Cell 29 February 2024 187(5):1296-1311

Optimal estimates of diffusion coefficients from molecular dynamics simulations

Authors: Bullerjahn, Jakob Tómas, von Bülow, Sören, Hummer, Gerhard

Subject Terms: Physics - Computational Physics, Condensed Matter - Statistical Mechanics, Physics - Biological Physics

Access URL: http://arxiv.org/abs/2003.09193

Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure

Authors: von Bülow, Sören, Bullerjahn, Jakob Tómas, Hummer, Gerhard

Subject Terms: Physics - Computational Physics, Condensed Matter - Statistical Mechanics, Physics - Biological Physics

Access URL: http://arxiv.org/abs/2003.09205

Prediction of phase-separation propensities of disordered proteins from sequence.

Authors: von Bülow, Sören¹ soren.bulow@bio.ku.dk, Tesei, Giulio¹, Zaidi, Fatima Kamal², Mittag, Tanja², Lindorff-Larsen, Kresten¹ lindorff@bio.ku.dk

Source: Proceedings of the National Academy of Sciences of the United States of America. 4/1/2025, Vol. 122 Issue 13, p1-11. 37p.

Subject Terms: *RNA regulation, *PHASE separation, *PROTEIN fractionation, *MOLECULAR dynamics, *INTERMOLECULAR interactions

Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates.

Authors: Yasuda, Ikki, von Bülow, Sören, Tesei, Giulio, Yamamoto, Eiji, Yasuoka, Kenji, Lindorff-Larsen, Kresten

Source: Journal of Chemical Theory & Computation; 3/11/2025, Vol. 21 Issue 5, p2766-2779, 14p

Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC

Authors: Sušac, Lukas, Vuong, Mai T., Thomas, Christoph, von Bülow, Sören, O’Brien-Ball, Caitlin, Santos, Ana Mafalda, Fernandes, Ricardo A., Hummer, Gerhard, Tampé, Robert, Davis, Simon J.

Source: In Cell 18 August 2022 185(17):3201-3213

Structural basis of polyamine transport by human ATP13A2 (PARK9)

Authors: Sim, Sue Im, von Bülow, Sören, Hummer, Gerhard, Park, Eunyong

Source: In Molecular Cell 18 November 2021 81(22):4635-4649

MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins.

Authors: Piovesan, Damiano, Del Conte, Alessio, Mehdiabadi, Mahta, Aspromonte, Maria Cristina, Blum, Matthias, Tesei, Giulio, von Bülow, Sören, Lindorff-Larsen, Kresten, Tosatto, Silvio C E

Source: Nucleic Acids Research; 1/6/2025, Vol. 53 Issue D1, pD495-D503, 9p

Dynamic cluster formation determines viscosity and diffusion in dense protein solutions

Authors: von Bülow, Sören, Siggel, Marc, Linke, Max, Hummer, Gerhard

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 May . 116(20), 9843-9852.

Access URL: https://www.jstor.org/stable/26705222

A coarse‐grained model for disordered and multi‐domain proteins.

Authors: Cao, Fan, von Bülow, Sören, Tesei, Giulio, Lindorff‐Larsen, Kresten

Source: Protein Science: A Publication of the Protein Society; Nov2024, Vol. 33 Issue 11, p1-14, 14p

Structure and dynamics of the platelet integrin-binding C4 domain of von Willebrand factor

Authors: Xu, Emma-Ruoqi ^*, von Bülow, Sören ^*, Chen, Po-Chia, Lenting, Peter J., Kolšek, Katra, Aponte-Santamaría, Camilo, Simon, Bernd, Foot, Jaelle, Obser, Tobias, Schneppenheim, Reinhard, Gräter, Frauke, Denis, Cécile V., Wilmanns, Matthias ^*, Hennig, Janosch

Source: In Blood 24 January 2019 133(4):366-376

Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics

Authors: Chang, Chunmei, Young, Lindsey N., Morris, Kyle L., von Bülow, Sören, Schöneberg, Johannes, Yamamoto-Imoto, Hitomi, Oe, Yukako, Yamamoto, Kentaro, Nakamura, Shuhei, Stjepanovic, Goran, Hummer, Gerhard, Yoshimori, Tamotsu, Hurley, James H.

Source: In Molecular Cell 17 January 2019 73(2):339-353

Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants.

Authors: von Bülow, Sören¹ (AUTHOR), Sikora, Mateusz^1,2 (AUTHOR), Blanc, Florian E. C.¹ (AUTHOR), Covino, Roberto³ (AUTHOR), Hummer, Gerhard^1,4 (AUTHOR) gerhard.hummer@biophys.mpg.de

Source: PLoS Computational Biology. 1/24/2023, Vol. 19 Issue 1, p1-15. 15p. 1 Color Photograph, 1 Diagram, 2 Charts, 3 Graphs.

Subject Terms: *SARS-CoV-2, *MOLECULAR dynamics, *SARS-CoV-2 Omicron variant, *VACCINE effectiveness, *IMMUNOGLOBULINS, *AVIAN influenza

Insights into the conservation and diversification of the molecular functions of YTHDF proteins.

Authors: Flores-Téllez, Daniel^1,2, Tankmar, Mathias Due¹, von Bülow, Sören¹, Chen, Junyu¹, Lindorff-Larsen, Kresten¹, Brodersen, Peter¹, pbrodersen@bio.ku.dk, Arribas-Hernández, Laura¹, pbrodersen@bio.ku.dk

Source: PLoS Genetics; 10/10/2023, Vol. 19 Issue 10, p1-37, 37p

Computational epitope map of SARS-CoV-2 spike protein.

Authors: Sikora, Mateusz^1,2 (AUTHOR), von Bülow, Sören¹ (AUTHOR), Blanc, Florian E. C.¹ (AUTHOR), Gecht, Michael¹ (AUTHOR), Covino, Roberto^1,3 (AUTHOR), Hummer, Gerhard^1,4 (AUTHOR) gerhard.hummer@biophys.mpg.de

Source: PLoS Computational Biology. 4/1/2021, Vol. 17 Issue 4, p1-16. 16p. 4 Diagrams, 1 Chart, 1 Graph.

Subject Terms: *MOLECULAR dynamics, *SARS-CoV-2, *COAT proteins (Viruses), *COVID-19 vaccines, *VIRAL envelopes, *STRUCTURAL dynamics, *GLYCANS, *VIRAL envelope proteins

Optimal estimates of self-diffusion coefficients from molecular dynamics simulations.

Authors: Bullerjahn, Jakob Tómas, von Bülow, Sören, Hummer, Gerhard

Source: Journal of Chemical Physics; 7/14/2020, Vol. 153 Issue 2, p1-13, 13p, 6 Graphs

Subject Terms: DIFFUSION coefficients, MOLECULAR dynamics, COMPLEX fluids, PYTHON programming language, SIMULATION software, ESTIMATES

Plant YTHDF proteins are direct effectors of antiviral immunity against an N6‐methyladenosine‐containing RNA virus.

Authors: Martínez‐Pérez, Mireya, Aparicio, Frederic, Arribas‐Hernández, Laura, Tankmar, Mathias Due, Rennie, Sarah, von Bülow, Sören, Lindorff‐Larsen, Kresten, Brodersen, Peter, Pallas, Vicente

Source: EMBO Journal; 9/18/2023, Vol. 42 Issue 18, p1-17, 17p

Subject Terms: PLANT proteins, RNA viruses, PLANT RNA, RNA interference, MOSAIC viruses, DOUBLE-stranded RNA