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Atomistic molecular dynamics simulations of peptide-glycosaminoglycan binding were conducted with the pmemd program in the Amber suite software suite (http://ambermd.org).org
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Five days past-confluence I-VEGF/VEGFf binding was conducted with isolated ECM.
To confirm the residues localized within N150 V164 of FlpA-D2 are required for Fn-binding, binding assays were conducted with a set of new peptides (NP1 9) of 12 residues.
Since DNA-binding sites for CREB, Sp1, AP1 and AP2 have been putatively described in the NIS promoter region [ 5], competitive binding studies were conducted with synthetic 22-mer double stranded synthetic oligonucleotides containing DNA-binding sites for each of these transcription factors.
Nuclear extract preparation and NF-κB DNA binding experiments were conducted with kits purchased from Active Motif.
Latex beads were coated with fibronectin (McKeown et al., 1990) and bead binding assays were conducted with DDR1 wild type, knockdown and over-expressing cells.
SPR binding studies were conducted with 5′-biotinated DNAs as previously described, while spectroscopic studies were performed with non-biotin-labeled DNAs.
Cyanide binding experiments were conducted with a stopped-flow apparatus (model SX-18MV, Applied Photophysics) equipped for both conventional and sequential measurements.
The binding reactions were conducted with 5 μg of nuclear extract and of 2 × 105 cpm of [γ-P]-labeled oligonucleotide probe at 22°C for 20 minutes in a final volume of 10 μl, and complexes were resolved on non-denaturing 6% polyacrylamide gels.
CCKR-binding assays were conducted with 3H-CCK-8 (propiony-3H-sulfated and propionylated CCK-8, 93.0 Ci/mmol; Amersham Pharmacia Radiochemicals) to determine the CCKR binding activity in both the hippocampus and amygdala as described previously [12].
In vitro binding assays for VAChT were conducted with human VAChT stably expressed in PC12A123.7 cells at about 50 pmol/mg of crude extract.
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