Related papers: PhosNetVis: a web-based tool for fast kinase-subst…
Protein phosphorylation is a reversible post-translational modification commonly used by cell signaling networks to transmit information about the extracellular environment into intracellular organelles for the regulation of the activity…
Phosphorylation site prediction based on kinase-substrate interaction plays a vital role in understanding cellular signaling pathways and disease mechanisms. Computational methods for this task can be categorized into kinase-family-focused…
The human proteome contains a vast network of interacting kinases and substrates. Even though some kinases have proven to be immensely useful as therapeutic targets, a majority are still understudied. In this work, we present a novel…
We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…
Image fusion helps in merging two or more images to construct a more informative single fused image. Recently, unsupervised learning based convolutional neural networks (CNN) have been utilized for different types of image fusion tasks such…
Multisite protein phosphorylation plays a pivotal role in regulating cellular signaling and decision-making processes. In this study, we focus on the mathematical underpinnings and informational aspects of sequential, distributive…
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital…
GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based…
The Protein Secondary Structure Visualizer ProS2Vi is a novel Python-based visualization tool designed to enhance the analysis and accessibility of protein secondary structures calculated and identified by the Dictionary of Secondary…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to…
Post-translational modifications (PTMs) have vital roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a…
Motivation: Network visualizations of complex biological datasets usually result in 'hairball' images, which do not discriminate network modules. Results: We present the EntOptLayout Cytoscape plug-in based on a recently developed network…
Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
This paper proposes a web-based visual graph analytics platform for interactive graph mining, visualization, and real-time exploration of networks. GraphVis is fast, intuitive, and flexible, combining interactive visualizations with…
As the size of accessible compound libraries expands to over 10 billion, the need for more efficient structure-based virtual screening methods is emerging. Different pre-screening methods have been developed for rapid screening, but there…
Drug discovery represents a time-consuming and financially intensive process, and virtual screening can accelerate it. Scoring functions, as one of the tools guiding virtual screening, have their precision closely tied to screening…
Lensless imaging stands out as a promising alternative to conventional lens-based systems, particularly in scenarios demanding ultracompact form factors and cost-effective architectures. However, such systems are fundamentally governed by…
Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have…