Search Results for "atomic distance"
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Showing 5 open source projects for "atomic distance"
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1
Alphafold2
Unofficial Pytorch implementation / replication of Alphafold2
... 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. -
2
MoleculeViewer
View 3D molecule structure and plot 2D density map for CRYSTAL program
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 : zoom Left... -
3
ppienergy
Compute Protein Protein Interaction Energy Profile
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... -
4
ForceReader
Soft for force spectroscopy data analysis
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. -
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5
BondInfo
BondInfo - a program for interatomic distances analysis
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)
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