Related papers: pdbmine: A Node.js API for the RCSB Protein Data B…
Designing flexible graph kernels that can run well on various platforms is a crucial research problem due to the frequent usage of graphs for modeling data and recent architectural advances and variety. In this work, we propose a novel…
The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures challenge users in computational biology for utilizing the structural information and protein surface property…
Distributed data processing platforms such as MapReduce and Pregel have substantially simplified the design and deployment of certain classes of distributed graph analytics algorithms. However, these platforms do not represent a good match…
JavaScript engines inside modern browsers are capable of running sophisticated multi-player games, rendering impressive 3D scenes, and supporting complex, interactive visualizations. Can this processing power be harnessed for information…
Nowadays, many scientific areas share the same broad requirements of being able to deal with massive and distributed datasets while, when possible, being integrated with services and applications. In order to solve the growing gap between…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
Protein engineering is important for biomedical applications, but conventional approaches are often inefficient and resource-intensive. While deep learning (DL) models have shown promise, their training or implementation into protein…
DuckDB is designed for portability. It is also designed to run anywhere, and possibly in contexts where it can be specialized for performance, e.g., as a cloud service or on a smart device. In this paper, we consider the way DuckDB…
Deep learning can achieve outstanding results in various fields. However, it requires so significant computational power that graphics processing units (GPUs) and/or numerous computers are often required for the practical application. We…
Graph mining applications, such as subgraph pattern matching and mining, are widely used in real-world domains such as bioinformatics, social network analysis, and computer vision. Such applications are considered a new class of…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
Graph theory and graph mining constitute rich fields of computational techniques to study the structures, topologies and properties of graphs. These techniques constitute a good asset in bioinformatics if there exist efficient methods for…
Persistent or Non Volatile Memory (PMEM or NVM) has recently become commercially available under several configurations with different purposes and goals. Despite the attention to the topic, we are not aware of a comprehensive empirical…
When developing a (web) interface for a deductive database, functionality required by the client is provided by means of HTTP handlers that wrap the logical data access predicates. These handlers are responsible for converting between…
Social media is a biggest successful buzzword used in the recent time. Its success opened various opportunities for the developers. Developing any application requires storage of large data into databases. Many databases are available for…
Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…
The Protein Data Bank (PDB) contains the atomic structures of over 105 biomolecules with better than 2.8A resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the…
The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Data cubes are used for analyzing large data sets usually contained in data warehouses. The most popular data cube tools use graphical user interfaces (GUI) to do the data analysis. Traditionally this was fine since data analysts were not…