Related papers: Identifying metabolites from protein identifiers w…
Post-translational modifications (PTMs) serve as a dynamic chemical language regulating protein function, yet current proteomic methods remain blind to a vast portion of the modified proteome. Standard database search algorithms suffer from…
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…
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…
Background. Emerging technologies now allow for mass spectrometry based profiling of up to thousands of small molecule metabolites (metabolomics) in an increasing number of biosamples. While offering great promise for revealing insight into…
The detailed analysis of molecular structures and properties holds great potential for drug development discovery through machine learning. Developing an emergent property in the model to understand molecules would broaden the horizons for…
Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We…
SMILES is a linear representation of chemical structures which encodes the connection table, and the stereochemistry of a molecule as a line of text with a grammar structure denoting atoms, bonds, rings and chains, and this information can…
Identifying potential drug targets using metabolic modeling requires integrating multiple modeling methods and heterogenous biological datasets, which can be challenging without sophisticated tools. We developed COMO, a user-friendly…
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…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein…
The unbounded permutations of biological molecules, including proteins and their constituent peptides, presents a dilemma in identifying the components of complex biosamples. Sequence search algorithms used to identify peptide spectra can…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
Summary: Integration of multi-omics data on chemical exposure of cells or organisms promises a more complete representation of the responding pathways than single omics data. Data of different omics layers, like transcriptome or proteome is…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
Comprehensive and confident identifications of metabolites and other chemicals in complex samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent advances,…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…