Sentence examples for remove clashes from inspiring English sources
To answer this question, the crystal structure poses were rescored following the same procedure as above, with a slight optimization to remove clashes, and ranked among the other poses.
Like for the native interactions, we then relaxed the new interaction pairs using the strong force field option to remove clashes and compute the binding energies with the less strict force field (VdWDesign = 0).
The models were then protonated under SYBYL version 6.9 (Tripos Associates, St . Louis MO, USA), and subject to brief energy minimization (20 steps steepest descent, followed by 20 steps conjugate gradients) employing the Tripos forcefield [48] under SYBYL v6.9 to remove clashes and bad geometries.
The resulting crude model was manually rebuilt to remove clashes where possible and finally energy-minimised using GROMACS (Lindahl et al, 2001) with a simulated annealing protocol.
This was followed by energy minimization to remove clashes, assignment of initial velocities from a Maxwell distribution, and 1 ns of solvent equilibration in which the positions of heavy protein and DNA atoms were restrained.
In the second phase, the lowest-energy complex predicted by molecular docking was subjected to 1000 steps of energy minimization by using the perl script of minAmber MMTSB_tool for removing clashes and refining complex docked by using an Amber-based procedure [38].
The dimeric models were minimized for 2000 steps to remove structural clashes using the conjugate gradient algorithm.
The side chains of newly introduced amino acid residues were manually adjusted to remove local clashes and to allow potential hydrogen bonding and electrostatic interactions.
The initial molecular conformations for the adducts were subjected to a constrained energy minimization step in order to remove steric clashes.
See the FlexPepDockAbInitio protocol capture archive: scripts/prep_abinitio.sh pdb-id A first preliminary step in our protocol involves the packing of the side-chains in each monomer to remove internal clashes that are not related to inter-molecular interactions, as described in Raveh et al. [26].
The AT lipids were then energy-minimized to remove any clashes that resulted from the conversion.
