Search Results for "determination of atomic distance"

... a straight pytorch translation with some improvements on positional encoding. lhatsk has reported training a modified trunk of this repository, using the same setup as trRosetta, with competitive results. The underlying assumption is that the trunk works on the residue level, and then constitutes to atomic level for the structure module, whether it be SE3 Transformers, E(n)-Transformer, or EGNN doing the refinement.

Identification of clines from allele frequency or genome-wide databases. Angular transformation. Sigmoid function. Parameterization of a cline: orientation, Pearson’s product-moment correlation coefficient, linear and sigmoid regression and coefficient of determination. Graphical representation of the cline. Confidence limits. Spatial autocorrelation. Moran's index. Isolation by distance. Exponential regression. Correlation Fst/Distance. Centroid method. Cline's expected vs. predicted...

Crystallographic shell-waters that originate from diffraction data are an essential component, but not bulk water, of protein structure and stability. It interacts with various polar and non-polar components of protein. Polar backbone is constituted by O-type and N-type atoms of all residues. Polar side-chains are O, N, S containing groups of amino acid residues. Notably, ordered shell-waters form bridge interactions. Disordered shell-water may occupy central hydrophobic-cavity of protein....

A Java sotware for viewing 3D molecule structure and plotting 2D density map. The atomic positions (coordinates) are read from files for the CRYSTAL and GAUSSIAN programs. Supported files: 1. *.xyz (molecule cartesian coordinates file) 2. *.gjf (GAUSSIAN's input file) 3. *.out (CRYSTAL98&2k's scf or properties output file) 4. fort.25 (CRYSTAL98&2k's ECHG(Electronic Charge Density) outpit file with fort.25 format). Molecule's 3D operations: Left drag : free rotate Right drag...

Protein-protein interactions (PPIs) are crucial for understanding the signaling and disease mechanisms in a cell. In the present work, we have developed a new approach to explore the energy landscape of protein-protein interactions by employing a rapid modified DFT-D approach using the atomic coordinates obtained from X-ray and NMR spectroscopy data. The distance energy plots of contact residues in the interacting regions of several experimentally validated protein-protein complexes were...

An EDM calibration baseline is used to derive specific instrument errors of the electronic distance measurement (EDM) unit of a total station. EDMFit is a simple adjustment tool to estimate the EDM calibration parameters (addition constant and/or scale parameter). The adjustment process is according to ISO 17123-4. The parameters are checked for significance, to avoid an overestimation. Based on two classical hypothesis testing, EDMFit provides a reliable outlier detection

A simple Windows application for data of atomic force spectroscopy (force-distance curves) analysis. It is adopted for Veeco/Bruker Picoforce file format, but it is possible to use it for analysis of txt-table data.

BondInfo is used for analysis of interatomic distances using atomic, covalent radii of the elements and electronegativity. A possibility to analyse the distances between two sites with statistical mixtures of two atoms is avaliable. BondInfo calculates the relative contribution of covalent, ionic, and metallic bonding between 2 atoms (or statistical mixtures)