Related papers: BEER: Biochemical Estimator and Explorer of Residu…
We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the…
Identifying differentially expressed genes from RNA sequencing data remains a challenging task because of the considerable uncertainties in parameter estimation and the small sample sizes in typical applications. Here we introduce Bayesian…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…
BEIR is a benchmark dataset for zero-shot evaluation of information retrieval models across 18 different domain/task combinations. In recent years, we have witnessed the growing popularity of a representation learning approach to building…
Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for…
Food protein digestibility and bioavailability are critical aspects in addressing human nutritional demands, particularly when seeking sustainable alternatives to animal-based proteins. In this study, we propose a machine learning approach…
The performance evaluation of biometric systems is a crucial step when designing and evaluating such systems. The evaluation process uses the Equal Error Rate (EER) metric proposed by the International Organization for Standardization…
Identifying the relations between chemicals and proteins is an important text mining task. BioCreative VII track 1 DrugProt task aims to promote the development and evaluation of systems that can automatically detect relations between…
Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" become a verb, describing the act of performing sequence search and alignment. However, if one needs…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Accurate information about protein content in the organism is instrumental for a better understanding of human biology and disease mechanisms. While the presence of certain types of proteins can be life-threatening, the abundance of others…
Understanding protein function at the molecular level requires connecting residue-level annotations with physical and structural properties. This can be cumbersome and error-prone when functional annotation, computation of physico-chemical…
Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already…
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…
Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…
Decoding protein-protein interactions (PPIs) at the residue level is crucial for understanding cellular mechanisms and developing targeted therapeutics. We present Seq2Bind Webserver, a computational framework that leverages fine-tuned…
We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based…
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…
A new software package, the Fission Induced Electromagnetic Response (FIER) code, has been developed to analytically predict delayed $\gamma$-ray spectra following fission. FIER uses evaluated nuclear data and solutions to the Bateman…