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AI-based in silico methods have improved protein structure prediction but often struggle with large protein complexes (PCs) involving multiple interacting proteins due to missing 3D spatial cues. Experimental techniques like Cryo-EM are…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…
A tight binding model for scanning tunneling microscopy images of a molecule adsorbed on a metal surface is described. The model is similar in spirit to that used to analyze conduction along molecular wires connecting two metal leads and…
We present a novel method for the automatic detection of pockets on protein molecular surfaces. The algorithm is based on an ad hoc hierarchical clustering of virtual SES probe spheres obtained from the geometrical primitives generated by…
Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
Nuclear spins are among the potential candidates prospected for quantum information technology. A recent breakthrough enabled to atomically resolve their interaction with the electron spin, the so-called hyperfine interaction, within…
We investigate quantum spectroscopy with undetected photons for protein detection in the mid-infrared spectral region. Classical Fourier-transform infrared spectroscopy of protein samples (bovine serum albumin and N-terminal pro-brain…
From the spread of pollutants in the atmosphere to the transmission of nutrients across cell membranes, anomalous diffusion processes are ubiquitous in natural systems. The ability to understand and control the mechanisms guiding such…
Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…
Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
Multi-technique high resolution X-ray mapping enhanced by the recent advent of 4th generation synchrotron facilities can produce colossal datasets, challenging traditional analysis methods. Such difficulty is clearly materialized when…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
Protein-surface interactions cause the desirable effect of controlled protein adsorption onto biodevices as well as the undesirable effect of protein fouling. The key to controlling protein-surface adsorptions is to identify and quantify…