Related papers: Fast Proteome Identification and Quantification fr…
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a…
Domain adaptation (DA) is an important technique for modern machine learning-based medical data analysis, which aims at reducing distribution differences between different medical datasets. A proper domain adaptation method can…
High-dimensional data requires scalable algorithms. We propose and analyze three scalable and related algorithms for semi-supervised discriminant analysis (SDA). These methods are based on Krylov subspace methods which exploit the data…
Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…
Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet…
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…
Due to the highly complex chemical structure of biomolecules, the extensive understanding of the electronic information for proteomics can be challenging. Here, we constructed a charge transfer database at residue level derived from…
Small-molecule drug discovery requires simultaneous optimization of numerous properties of candidate molecules. These properties can be investigated through the analysis of high-dimensional biological signatures, such as cell morphology and…
Proteins are the active working horses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now…
Efficient encoding and representation of large 3D molecular structures with high fidelity is critical for biomolecular design applications. Despite this, many representation learning approaches restrict themselves to modeling smaller…
Domain Adaptation (DA) techniques are important for overcoming the domain shift between the source domain used for training and the target domain where testing takes place. However, current DA methods assume that the entire target domain is…
The objective of this project is to develop an automated device used to spot protein samples on a hydrophobic membrane to be used for the patented electrophoresis method developed by Chang and Yonan in 2008 [1]. This novel method performs…
Virtual screening of small molecules against protein targets can accelerate drug discovery and development by predicting drug-target interactions (DTIs). However, structure-based methods like molecular docking are too slow to allow for…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
Accurate cell counting in microscopic images is important for medical diagnoses and biological studies. However, manual cell counting is very time-consuming, tedious, and prone to subjective errors. We propose a new density regression-based…
We theorize that phylogenetic profiles provide a quantitative method that can relate the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of phylogenetic profiles is the…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across…