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1701 Publications visible to you, out of a total of 1701
Type Ia supernova progenitors: a contemporary view of a long-standing puzzle

Abstract

Not specified

Authors: Ashley Jade Ruiter, Ivo Rolf Seitenzahl

Date Published: 1st Dec 2025

Publication Type: Journal

Distanzbasierte Inferenz von Genbäumen unter Berücksichtigung ihres Speziesbaumes

Abstract (Expand)

In dieser Arbeit wird Spearfish, eine neue Methode zur distanzbasierten Inferenz von Genbäumen, entwickelt und getestet. Spearfish verwendet die paarweisen Distanzen der Gensequenzen, sowie die Distanzen … der zugehörigen Spezies im Speziesbaum, in einem Clustering-Verfahren, um 10 Genbäume zu rekonstruieren. Der beste wird anschließend mithilfe eines statistischen Evaluierungsverfahrens ausgewählt. Auf allen getesteten simulierten Datensätzen konnte gezeigt werden, dass die von Spearfish inferierten Bäume durchschnittlich eine Distanz von 0,213 zum echten Genbaum besitzen. Damit ist es 2,18-mal genauer als Methoden wie RAxML-NG, welche den Speziesbaum nicht berücksichtigen. Spearfish ist 25,85% ungenauer, aber 49,63% schneller als GeneRax, eine der führenden Methoden, die Genbäume mithilfe ihres Speziesbaumes korrigieren. So kann Spearfish verwendet werden, um Startbäume für GeneRax zu rekonstruieren oder bei goßen Datensätzen sogar zu ersetzen.

Authors: Lukas Knirsch, Benoit Morel, Alexandros Stamatakis

Date Published: 2nd Oct 2025

Publication Type: Bachelor's Thesis

Simulation of Neurotrophin Receptor Transmembrane Helix Interactions Reveals Active States and Distinct Signaling Mechanisms

Abstract

Not specified

Authors: Christina Athanasiou, Ainara Claveras Cabezudo, Alexandros Tsengenes, Rebecca C. Wade

Date Published: 27th Apr 2025

Publication Type: Journal

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning

Abstract (Expand)

The design of proteins capable effectively binding to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a …we introduce a complementarity-determining region (CDR) grafting approach for designing nanobodies (Nbs) that target specific epitopes, with the aid of computer simulation and machine learning. As a proof-of-concept, we designed, evaluated, and characterized a high-affinity Nb against the spike protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. The designed Nb, referred to as Nb Ab.2, was synthesized and displayed high-affinity for both the purified receptor-binding domain protein and to the virus-like particle, demonstrating affinities of 9 nM and 60 nM, respectively, as measured with microscale thermophoresis. Circular dichroism showed the designed protein’s structural integrity and its proper folding, whereas molecular dynamics simulations provided insights into the internal dynamics of Nb Ab.2. This study shows that our computational pipeline can be used to efficiently design high-affinity Nbs with diagnostic and prophylactic potential, which can be tailored to tackle different viral targets.

Authors: Matheus VF Ferraz, W Camilla S Adan, Tayná E Lima, Adriele JC Santos, Sérgio O de Paula, Rafael Dhalia, Gabriel L Wallau, Rebecca C Wade, Isabelle FT Viana, Roberto D Lins

Date Published: 21st Apr 2025

Publication Type: Journal

Prediction of drug-protein binding kinetics

Abstract

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Author: Abraham Muñiz‐Chicharro

Date Published: 3rd Apr 2025

Publication Type: Doctoral Thesis

The need to implement FAIR principles in biomolecular simulations.

Abstract

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Authors: R. E. Amaro, J. Aqvist, I. Bahar, F. Battistini, A. Bellaiche, D. Beltran, P. C. Biggin, M. Bonomi, G. R. Bowman, R. A. Bryce, G. Bussi, P. Carloni, D. A. Case, A. Cavalli, C. A. Chang, T. E. 3rd Cheatham, M. S. Cheung, C. Chipot, L. T. Chong, P. Choudhary, G. A. Cisneros, C. Clementi, R. Collepardo-Guevara, P. Coveney, R. Covino, T. D. Crawford, M. Dal Peraro, B. L. de Groot, L. Delemotte, M. De Vivo, J. W. Essex, F. Fraternali, J. Gao, J. L. Gelpi, F. L. Gervasio, F. D. Gonzalez-Nilo, H. Grubmuller, M. G. Guenza, H. V. Guzman, S. Harris, T. Head-Gordon, R. Hernandez, A. Hospital, N. Huang, X. Huang, G. Hummer, J. Iglesias-Fernandez, J. H. Jensen, S. Jha, W. Jiao, W. L. Jorgensen, S. C. L. Kamerlin, S. Khalid, C. Laughton, M. Levitt, V. Limongelli, E. Lindahl, K. Lindorff-Larsen, S. Loverde, M. Lundborg, Y. L. Luo, F. J. Luque, C. I. Lynch, A. D. Jr MacKerell, A. Magistrato, S. J. Marrink, H. Martin, J. A. McCammon, K. Merz, V. Moliner, A. J. Mulholland, S. Murad, A. N. Naganathan, S. Nangia, F. Noe, A. Noy, J. Olah, M. L. O'Mara, M. J. Ondrechen, J. N. Onuchic, A. Onufriev, S. Osuna, G. Palermo, A. R. Panchenko, S. Pantano, C. Parish, M. Parrinello, A. Perez, T. Perez-Acle, J. R. Perilla, B. M. Pettitt, A. Pietropaolo, J. P. Piquemal, A. B. Poma, M. Praprotnik, M. J. Ramos, P. Ren, N. Reuter, A. Roitberg, E. Rosta, C. Rovira, B. Roux, U. Rothlisberger, K. Y. Sanbonmatsu, T. Schlick, A. K. Shaytan, C. Simmerling, J. C. Smith, Y. Sugita, K. Swiderek, M. Taiji, P. Tao, D. P. Tieleman, I. G. Tikhonova, J. Tirado-Rives, I. Tunon, M. W. van der Kamp, D. van der Spoel, S. Velankar, G. A. Voth, R. Wade, A. Warshel, V. V. Welborn, S. D. Wetmore, T. J. Wheeler, C. F. Wong, L. W. Yang, M. Zacharias, M. Orozco

Date Published: 2nd Apr 2025

Publication Type: Journal

The BeeProject: Advanced Digitisation and Creation of a Dataset for the Monitoring of Beehives

Abstract (Expand)

The digitisation of historical documents, particularly those containing tabular data, is becoming increasingly critical for the preservation of information and analysis of long-term trends. However, … this task presents significant challenges, particularly with semi-formal documents like handwritten records, which often need more consistent structure. This paper addresses the challenge of developing an automated approach for transcribing historical handwritten tables. Our presented method works on a mixture of computer vision tools and optical character recognition (OCR) to detect the grid and content of the table. The dataset we collected contains records from beekeepers, consisting of hive weight gain and loss and meteorological conditions. The Institute of Bee Protection at JKI gathered this information from the German beekeeper associations of Lower Saxony, Hesse, Mecklenburg-Vorpommern, Thuringia, and Brandenburg in Germany within the collaborative research project MonViA. This data is crucial for understanding the impact of climate change on bee vitality and contains daily information from each beekeeper over decades, holding valuable insights into past environmental conditions. The success rate of automatically transcribed hive scale data from Lower Saxony was compared with the accuracy of transcription done by human power. Our dataset of 14\,738 handwritten scans, out of which 3819 were manually digitised, provides a large ground truth for future research, paving the way for further exploration and uncovering other historical knowledge.

Authors: Lukrécia Mertová, Severin Polreich, Oleg Lewkovski, Wolfgang Müller

Date Published: 13th Mar 2025

Publication Type: InProceedings

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