相关论文: A Structured Hardware Software Architecture for Pe…
The problem of inferring proteins from complex peptide samples in shotgun proteomic workflow sets extreme demands on computational resources. This is exacerbated by the fact that, in general, a given protein cannot be defined by a fixed…
Protein inference plays a vital role in the proteomics study. Two major approaches could be used to handle the problem of protein inference; top-down and bottom-up. This paper presents a framework for protein inference, which uses hardware…
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…
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…
Protein design has the potential to revolutionize biotechnology and medicine. While most efforts have focused on proteins with well-defined structures, increased recognition of the functional significance of intrinsically disordered…
Protein structure prediction is a challenging and unsolved problem in computer science. Proteins are the sequence of amino acids connected together by single peptide bond. The combinations of the twenty primary amino acids are the…
Accurately predicting protein structures from amino acid sequences remains a fundamental challenge in computational biology, with profound implications for understanding biological functions and enabling structure-based drug discovery.…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…
It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a…
Protein structure generative models excel at predicting single protein static structures from sequence, but routinely fail to capture the correct conformational state of protein complexes, critical for protein design and induced proximity…
Shotgun proteomics is a high-throughput technology used to identify unknown proteins in a complex mixture. At the heart of this process is a prediction task, the spectrum identification problem, in which each fragmentation spectrum produced…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
By coupling peptides with DNA tags (i.e., 'barcodes'), it is now possible to harness high-throughput sequencing (HTS) technologies to enable highly multiplexed peptide-based assays, which have a variety of potential applications including…
Mass spectrometry-based proteomics is a key enabler for personalized healthcare, providing a deep dive into the complex protein compositions of biological systems. This technology has vast applications in biotechnology and biomedicine but…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…
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…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Recent advances in de novo protein binder design have enabled increasing experimental validation, yet reported in silico metrics remain difficult to interpret or compare across studies due to non-standardized evaluation protocols. We…
Addressing the growing demands of artificial intelligence (AI) and data analytics requires new computing approaches. In this paper, we propose a reconfigurable hardware accelerator designed specifically for AI and data-intensive…