We detect all functional groups contained in G using the open-source package RDKit41 and retrieve the corresponding functional group entities in ElementKG on the basis of their names. Then we obtain the embeddings of functional group entities {x1, …, xm} using the KG embedding method, ...
velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better samplin...
Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used. Important: only the bonds present in the ...
In realistic conditions of gas pressure and temperature, a high molecular coverage can be obtained, and when it is adsorbate covered, the surface/nanoparticle might be subject to strong reconstruction, completely modifying its geometry or even its composition. We will show that theoretical modeling ...
Lama5newborn cKO mice displayed reduced hair growth with defects in the tissue geometry of HG–DP interface (Supplementary Fig.8a, b). We investigated the continuum of hair cycle stages by observing hair cycle domain patterns on living mice39. In the mutants, the onset of the first catagen...
A single structure consistent with all of the spectral data was selected from the list of computer-generated structures. To the best of our knowledge, this is the first case of the application of an expert system to determine the molecular structure of a complex natural product which was not ...
This geometry is used to define the rigid constraints inTnum. The relevant parameters are the following: read_Qdyn0(defaultT): When the value isT, the reference geometry is defined with the dynamical coordinates (seeTnum). Remark, in previous version, this parameter was defined asread_Qsym0. ...
The system module has class definitions for components of molecular systems such as Particle, Bond, Angle, Dihedral, and Improper to help define bonding geometry in molecular models. Each of these items reference a type object (ParticleType, BondType, etc.) that defines force field parameters. ...
The list of compounds, their experimental and calculated data and 3D structures of the heat-of-sublimation calculations are available under the names of “S4. Experimental and Calculated Heat-of-Sublimation Data Table.doc” and “S5. Compounds List for Heat-of-Sublimation Calculations.sdf”. A ...
The Ramachandran plots of all the three shortlisted models were obtained using PROCHECK which evaluates the stereochemistry of protein models by determining residue-by-residue geometry and overall structure geometry [44]. A protein structure is considered as quality based on the percentage of residues ...