Related papers: Protein structure classification based on X-ray la…
Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the…
Precise control over interactions between ballistic electrons will enable us to exploit Coulomb interactions in novel ways, to develop high-speed sensing, to reach a non-linear regime in electron quantum optics and to realise schemes for…
We consider the Directed Coulomb Explosion regime of ion acceleration from ultra-thin double layer (high Z/low Z) mass limited targets. In this regime the laser pulse evacuated the electrons from the irradiated spot and accelerates the…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Realistic 3D-conformations of protein structures can be embedded in a cubic lattice using exclusively integer numbers, additions, subtractions and boolean operations.
The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow 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…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…
At the extreme energies of the Large Hadron Collider, massive particles can be produced at such high velocities that their hadronic decays are collimated and the resulting jets overlap. Deducing whether the substructure of an observed jet…
Enzymes and proteins are live driven biochemicals, which has a dramatic impact over the environment, in which it is active. So, therefore, it is highly looked-for to build such a robust and highly accurate automatic and computational model…
The problem of inferring proteins from complex peptide cocktails (digestion products of biological samples) in shotgun proteomic workflow sets extreme demands on computational resources in respect of the required very high processing…
We present a fingerprint-like method to analyze material defects after energetic particle irradiation by computing a rotation invariant descriptor vector for each atom of a given sample. For ordered solids this new method is easy to use,…
Quantum-chemical fragmentation methods offer an efficient approach for the treatment of large proteins, in particular if local target quantities such as protein--ligand interaction energies, enzymatic reaction energies, or spectroscopic…
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…
Algorithms that detect covariance between pairs of columns in multiple sequence alignments are commonly employed to predict functionally important residues and structural contacts. However, the assumption that co-variance only occurs…
We investigate the nuclear and the Coulomb contributions to the breakup cross sections of $^6$Li in collisions with targets in different mass ranges. Comparing cross sections for different targets at collision energies corresponding to the…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…