Sentence examples for molecular mechanics programs from inspiring English sources

Additionally, the GLYCAM nomenclature system can be implemented in other molecular mechanics programs such as GROMOS (Scott et al. 1999) and CHARMM (Brooks et al. 1983).

This naming convention, as well as the GLYCAM parameters, can be used with molecular mechanics programs that support AMBER input files (Case et al. 2005), including NAMD (Phillips et al. 2005) and NWChem (Kendall et al. 2000).

Interaction energies between enzymes and carbohydrate substrates were calculated after short energy minimization by a molecular mechanics program.

Bonding schemes for the different glucan sheets found in crystals of cellulose Iα and Iβ were analysed energetically with the molecular mechanics program, MM3.

Docking of taurolidine, taurultam and methylol-taurultam at the fimbriae active site was performed after mannose exclusion from the protein crystal structure using the molecular mechanics program CDOCKER.

The stereochemical parameters for CKI-7 used in subsequent refinement were based on the conformation of the inhibitor found in the crystal structure of casein kinase 1 (PDB ID 2CSN) [25] in conjunction with values from the energy minimized conformation obtained from the molecular mechanics program MM2 [37], [37] implemented in CambridgeSoft Chem3D software.

The initial coordinates of atoms in the structures under investigation were determined by molecular mechanics method using HyperChem7 program taking into account electrostatic and disperse forces between the cluster host (silica, polymer) and the guest molecule (articaine).

Detailed atomistic molecular models have been developed with the help of molecular mechanics and semi-empirical quantum mechanical calculations using Cerius and MOPAC V6.0 program packages and structural, volumetric, and mechanical properties, e.g. geometrical values, densities, have been calculated by simulations on these models.

We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192 212].

Quantum molecular mechanics simulations may help to explain the mechanism of proton transfer during 3′-processing.

We performed Sanger sequencing of 100 healthy controls and none harbored a c.104G>A mutation in exon 2 of COL9A3.> Molecular mechanics potential energy minimization and MD simulations were carried out using the program package AMBER 11 [ 9].