Related papers: Progress in the definition of a reference human mi…
In mass spectrometry-based proteomics, experts usually project data onto a single set of reference sequences, overlooking the influence of common haplotypes (combinations of genetic variants inherited together from a parent). We recently…
Mixture of parts model has been successfully applied to 2D human pose estimation problem either as explicitly trained body part model or as latent variables for the whole human body model. Mixture of parts model usually utilize tree…
In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
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…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence.…
Distinguishing one person from another (what biometricians call recognition) is extremely relevant for different aspects of life. Traditional biometric modalities (fingerprint, face, iris, voice) rely on unique, stable features that…
Objective and Impact Statement: Accurate organ segmentation is critical for many clinical applications at different clinical sites, which may have their specific application requirements that concern different organs. Introduction: However,…
An in-vitro cell culture system is used for biological discoveries and hypothesis-driven research on a particular cell type to understand mechanistic or test pharmaceutical drugs. Conventional in-vitro cultures have been applied to primary…
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and…
Multiple technologies that measure expression levels of protein mixtures in the human body offer a potential for detection and understanding the disease. The recent increase of these technologies prompts researchers to evaluate the…
Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale,…
Reproducibility is a cornerstone of science, as the replication of findings is the process through which they become knowledge. It is widely considered that many fields of science are undergoing a reproducibility crisis. This has led to the…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…
As protein informatics advances rapidly, the demand for enhanced predictive accuracy, structural analysis, and functional understanding has intensified. Transformer models, as powerful deep learning architectures, have demonstrated…
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…