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Search Results - algorithms

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Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both...
Published: 9/29/2023   |   Inventor(s): Eva Novoa, Morghan Lucas, Leszek Pryszcz, Rebeca Medina Azmecua
Keywords(s): Algorithms, Bioinformatics, Biomarkers, Diagnostics, Liquid Biopsy, Oncology
Category(s): Methodology, Software & Algorithms
ccSOL omics: large-scale prediction of protein solubility, aggregation and folding
The ccSOL webserver provides large-scale calculations for protein solubility using physical-chemical properties. In addition to the proteome wide identification of soluble fragments on a large scale, ccSOL omics also performs single-point mutations throughout the whole protein sequence to identify susceptible areas. Using information from coil/disorder...
Published: 3/19/2020   |   Inventor(s): Gian Gaetano Tartaglia, Federico Agostini, Davide Cirillo, Riccardo Delli Ponti, Petr Klus
Keywords(s): Algorithms, Bioinformatics, Protein Aggregation and Misfolding, Protein Solubility, Protein Structure & Design, Software
Category(s): Software & Algorithms
FoldX Suite - Protein Design Software
The FoldX Suite builds on the strong fundament of advanced protein design features, already implemented in the successful FoldX, and exploits the power of fragment libraries, by integrating in silico digested backbone protein fragments of different lengths. Such fragment-based strategy allows for new powerful capabilities: loop reconstruction, implemented...
Published: 5/15/2018   |   Inventor(s): Luis Serrano, Javier Delgado, François Stricher, Erik Verschueren, Peter Vanhee
Keywords(s): Algorithms, Bioinformatics, Protein Structure & Design, Software
Category(s): Software & Algorithms
catRAPID: large-scale sequence-based prediction of protein–RNA interactions
catRAPID estimates the binding propensity of protein-RNA pairs by using sequence information only. The algorithm can be used to predict protein associations with coding and non-coding transcripts. Predictions have proved very accurate (> 0.8) when validated by traditional Immunoprecipitation methods, like RIP and CLIP.Applications and Services:Identifies...
Published: 5/25/2020   |   Inventor(s): Gian Gaetano Tartaglia, Federico Agostini, Davide Cirillo, Petr Klus
Keywords(s): Algorithms, Bioinformatics, Biomarkers, Genomics, Protein Structure & Design, Software
Category(s): Software & Algorithms
Method to identify new cancer drug targets in spliceosomal components
A new method and tools to map functional interactions of spliceosomal components accurately captures known, and identify new physical and functional associations important for health and disease.The method can be used to infer targets for alternative splicing regulation, and to study the effects on splicing of compounds directed to altered, or disease-associated...
Published: 2/19/2019   |   Inventor(s): Juan Valcarcel, Juan Tejedor Vaquero, Panagiotis Papasaikas
Keywords(s): Algorithms, Bioinformatics, Genomics, Oncology
Category(s): Methodology, General Biology & Chemistry, Software & Algorithms

 

 

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