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Search · four archives
11 papers · ranked by Valyu relevance
Wei Zhang, Jonathan A Fine, Christopher Sculley, Jordon McGraw + 1 more
The representation of complex biomolecular structures and interactions is a difficult challenge across life sciences. Researchers and students use unintuitive 2D representations to gain an intuitive understanding of 3D space and molecular interactions. Since this is cumbersome for complex structures, such as…
Oscar O. Ortega, Carlos F. Lopez
Computational models of network-driven processes have become a standard to explain cellular systems-level behavior and predict cellular responses to perturbations. Modern models can span a broad range of biochemical reactions and species that, in principle, comprise the complexity of dynamic cellular processes.…
Muhammad Zain Butt, Rana Sheraz Ahmad, Eman Fatima, Muhammad Tahir ul Qamar
The application of Large Language Models (LLMs) for generating data visualizations through natural language interaction represents a promising advance in AI-assisted scientific analysis. However, existing LLM-based tools largely emphasize graph generation, while research workflows require not only visualization but…
Kirill Zinovjev, Marc W. van der Kamp
Motivation: Experimental structural data can allow detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than a static picture of protein-ligand interactions is obtained…
V. Chiara, A. Buatois, S.-Y. Kim
Video-tracking programs have now become an essential tool for researchers measuring animal behavior across biological fields. The panel of available programs is growing rapidly, providing researchers with numerous specific tools that will match their precise needs. However, their proliferation may complicate…
Nowlan H Freese, Karthik Raveendran, Chaitanya Kintali, Srishti Tiwari + 3 more
Visualization of genomic data is a key step in validating methods and results. Web-based science gateways such as CyVerse provide storage and analysis tools for genomic data but often lack visualization capability. Native, desktop visualization tools like Integrated Genome Browser enable highly interactive data…
Kirill Zinovjev, Marc W. van der Kamp
X-ray crystallography allows detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. However, crystal structures provide little more than a static picture of proteinligand interactions, whereas dynamical…
Fabien Campagne, William ER Digan, Manuele Simi
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast…
Althea Hansel-Harris, Andreas Tillack, Diogo Santos-Martins, Matthew Holcomb + 1 more
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large amounts of data proportional to the size of the compound library used, which must…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
Yann Spöri, Jean-François Flot
Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript and Python. Although Haxe is…