CHARMM


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CHARMMChemistry At Harvard Molecular Mechanics
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References in periodicals archive ?
Scheraga, "A comparison of the CHARMM, AMBER and ECEPP potentials for peptides.
A Novel Framework for Ab Initio Coarse Protein Structure Prediction
Development and current status of the CHARMM force field for nucleic acids.
Molecular analysis of alternative transcripts of equine AXL receptor tyrosine kinase gene
For the minimization, the CHARMM v27 force field was used with the conjugate gradient minimization scheme.
Trends in the Binding of Cell Penetrating Peptides to siRNA: A Molecular Docking Study
et al., "CHARMM: the biomolecular simulation program," Journal of Computational Chemistry, vol.
ProBLM web server: protein and membrane placement and orientation package
For obtaining topology file and parameters of small compounds, we employed SwissParam to generate these data and compatible with the CHARMM all atoms force field for GROMACS simulation.
Finding inhibitors of mutant superoxide dismutase-1 for amyotrophic lateral sclerosis therapy from traditional Chinese medicine
The minimization protocol employed the steepest descent method using BIO+, the HyperChem implementation of CHARMM (Chemistry at HARvard using Molecular Mechanics) force field (18), until the difference in energy after two consecutive iterations was less than 0.1 kcal/mol.
In silico evaluation of crosslinking effects on denaturant [m.sub.eq] values and [DELTA]Cp upon protein unfolding
The structural analysis of the proteins was done using Accelry's Discovery Studio [19] with 'smart minimizer' and CHARMm force field.
Insilico analysis of PAC-1 as an enhancer for caspase-3 to promote apoptosis
By using CHARMM, a molecular dynamics software, we performed a computer simulation of the protein Cyt1A from Bacillus thuringiensis var.
Chemistry and Chemical Engineering
ChemSketch also features molecular modelling applications which allow for 3-D rotation and for 3-D optimization of the structure using CHARMM parameterization.
Sketchy Details: Usinq the New ACD ChemSketch
[1994] for the widely used molecular mechanics and dynamics program CHARMM and was shown to be an efficient tool for the minimization of molecular potential functions in comparison to other available minimizers.
Remark on Algorithm 702--The Updated Truncated Newton Minimization Package
Examples include DYNA-3D and PRONTO-3D for structural mechanics modeling, GAUSSIAN and DMOL for quantum mechanical simulation of molecules, CHARMM and DISCOVER for molecular dynamics simulation for organic systems, and FIDAP for modeling complex fluid flows.
Massively parallel methods for engineering and science problems
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