Related papers: High throughput interactome determination via sulf…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
The large amount of powder diffraction data for which the corresponding crystal structures have not yet been identified suggests the existence of numerous undiscovered, physically relevant crystal structure prototypes. In this paper, we…
In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing…
Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81]…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
Autonomous synthesis and characterization of inorganic materials requires the automatic and accurate analysis of X-ray diffraction spectra. For this task, we designed a probabilistic deep learning algorithm to identify complex multi-phase…
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…
Direct dark matter detection focuses on elastic scattering of dark matter particles off nuclei. In this study, we explore inelastic scattering where the nucleus is excited to a low-lying state of 10-100 keV, with subsequent prompt…
The interaction of swift, free-space electrons with confined optical near fields has recently sparked much interest. It enables a new type of photon-induced near-field electron microscopy, mapping local optical near fields around…
Accurate prediction of protein-ligand binding affinity is crucial for rapid and efficient drug development. Recently, the importance of predicting binding affinity has led to increased attention on research that models the three-dimensional…
The adsorption of metal atoms on nanostructures, such as graphene and nanotubes, plays an important role in catalysis, electronic doping, and tuning material properties. Quantum chemical calculations permit the investigation of this process…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature…
The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…
We demonstrate that powder diffraction data can be collected from sub-micron crystals of a mbrane protein with nearly two orders of magnitude more atoms than the molecules commonly used for powder diffraction. The crystals of photosystem-1…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to…
Knowledge of molecular structure is paramount in understanding, and ultimately influencing, chemical reactivity. For nearly a century, diffractive imaging has been used to identify the structures of many biologically-relevant gas-phase…
In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural…