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Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
It has been a long-standing goal in machine learning, as well as in AI more generally, to develop life-long learning systems that learn many different tasks over time, and reuse insights from tasks learned, "learning to learn" as they do…
Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are…
Hydrogen bonds and other non-covalent interactions play a crucial role in maintaining the structural integrity and functionality of biological macromolecules such as proteins and nucleic acids. Accurate identification and analysis of these…
A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The…
Motivation: Assessing the match between two biomolecular structures is at the heart of structural analyses such as superposition, alignment and docking. These tasks are typically solved with specialized structure-matching techniques…
An amino acid insertion or deletion, or InDel, can have profound and varying functional impacts on a protein's structure. InDel mutations in the transmembrane conductor regulator protein for example give rise to cystic fibrosis.…
Protein-ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Tasks…
Local optimization of adsorption systems inherently involves different scales: within the substrate, within the molecule, and between molecule and substrate. In this work, we show how the explicit modeling of the different character of the…
We propose a novel method for establishing correspondence between two sequences of 2D images. One particular application of this technique is slice-level content navigation, where the goal is to localize specific 2D slices within a 3D…
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins.…
Quantum heuristics have shown promise in solving various optimization problems, including lattice protein folding. Equally relevant is the inverse problem, protein design, where one seeks sequences that fold to a given target structure. The…
In this article we present a machine learning model to obtain fast and accurate estimates of the molecular Hessian matrix. In this model, based on a random forest, the second derivatives of the energy with respect to redundant internal…
Deep Learning can significantly benefit cancer proteomics and genomics. In this study, we attempt to determine a set of critical proteins that are associated with the FLT3-ITD mutation in newly-diagnosed acute myeloid leukemia patients. A…
Multi-scale 3D characterization is widely used by materials scientists to further their understanding of the relationships between microscopic structure and macroscopic function. Scientific computed tomography (CT) instruments are one of…
Recent advances in protein large language models, such as ProtTeX, represent both side-chain amino acids and backbone structure as discrete token sequences of residue length. While this design enables unified modeling of multimodal protein…
The analysis of the internal structure of trees is highly important for both forest experts, biological scientists, and the wood industry. Traditionally, CT-scanners are considered as the most efficient way to get an accurate inner…
Correlations between two variables of a high-dimensional system can be indicative of an underlying interaction, but can also result from indirect effects. Inverse Ising inference is a method to distinguish one from the other. Essentially,…