Sentence examples for minimization protocol from inspiring English sources

The full-atom ligand structure was then minimized using the Q-MOL small molecule minimization protocol.

After the minimization protocol was executed, the in situ minimized ligands were stripped of their nonpolar hydrogens to simplify the overall view.

Random "raw" (not minimized) conformers generated by the MacroModel conformational search engine were used as input for a complex minimization protocol aiming at mimicking "real world" conditions, i.e. those, which a free, unbound ligand experiences in an aqueous environment represented by explicit water molecules.

Coulombic interactions were calculated as for the minimization protocol.

Additional refinements of the M antigen model were performed using a similar minimization protocol in which the type of residues constrained during the minimization were varied: initially, only residues out of the most favored regions of the Ramachandran plot were allowed to move, then residues with a high model B-factor and/or force field energy were included.

The same minimization protocol was used with both force fields.

The initial model was refined by alternating automatic minimization protocols performed with CNS inspecting visual electron density map and manually adjusted using the program O [37].

After addition of hydrogen atoms, the model was refined by energy minimization (EM) with the minimization protocols in the Discovery Studio 2.1 software package (Accelrys, San Diego, CA) using a CHARMm force field.

Alemtuzumab (Campath-1H), a fully humanized CD52-specific monoclonal antibody which profoundly depletes T, B and dendritic cells [13], [14], is also increasingly used as an immunosuppressive agent in solid organ transplantation, particularly in the setting of maintenance immunosuppression minimization protocols [15] [17].

On the other hand, minimization protocols are associated with progression of fibrosis, and noncompliance with the immunosuppressive regime constitutes a major risk factor for chronic humoral rejection.

The authors reviewed the different immunosuppressive protocols used in kidney transplantation, focusing in minimization protocols and their impact in kidney transplant fibrosis emphasizing the benefit to use calcineurin inhibitors, in particular tacrolimus.