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To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D…
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly…
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…
Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…
Transformation of protein 3D structures from their all-atom representation (AAR) to the double-centroid reduced representation (DCRR) is a prerequisite to the implementation of both the tetrahedral three-dimensional search motif (3D SM)…
Protein structure prediction has been a grand challenge problem in the structure biology over the last few decades. Protein quality assessment plays a very important role in protein structure prediction. In the paper, we propose a new…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
Experimental determination of protein function is resource-consuming. As an alternative, computational prediction of protein function has received attention. In this context, protein structural classification (PSC) can help, by allowing for…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence Alignments (MSAs) as inputs to learn the co-evolution information from…
The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary…
This survey for mathematicians summarizes several works by the author on protein geometry and protein function with applications to viral glycoproteins in general and the spike glycoprotein of the SARS-CoV-2 virus in particular. Background…
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…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
The detection of clinically significant prostate cancer lesions (csPCa) from biparametric magnetic resonance imaging (bp-MRI) has emerged as a noninvasive imaging technique for improving accurate diagnosis. Nevertheless, the analysis of…
Medical images acquired from standardized protocols show consistent macroscopic or microscopic anatomical structures, and these structures consist of composable/decomposable organs and tissues, but existing self-supervised learning (SSL)…
Recent development of high-resolution mass spectrometry (MS) instruments enables chemical cross-linking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…