Sentence examples for binding sites were modeled from inspiring English sources

Peptides and antibody binding sites were modeled as strings.

Iron and siderophore binding sites were modeled starting with RCSB Protein Data Bank structures 1Y9U A and 2OWT (to which hydrogens were added).1Y9U is the structure for the B. pertussis ferric binding protein in the apo (open) conformation.

Often, RBP-binding sites are modeled taking into account only sequential information.

Transcription factor binding sites are often modeled by Position Weighted Matrices (PWMs for short), also known as Position Specific Scoring Matrices (PSSMs for short), or simply matrices.

Sequencing reads were aligned to the genome using Bowtie [ 40] and binding sites were identified using the model-based analysis of ChIP-Seq (MACS) peak caller with an mfold cutoff of 15 [ 41].

Although one study used conventional APLs in collagen-induced arthritis [ 33], unconventional APLs with substitutions at MHC binding sites were mainly tested in arthritis models.

Using algorithms previously developed in the laboratory [ 70] binding sites were identified in the structural models for the set of EGs identified here.

Two putative binding sites were identified on the LeuTAa based model, one suggested to be a high-affinity site, and the other suggested to be a low-affinity binding site.

Five different protein models and active binding sites were predicted at significant cut-off confidence (C ≥ -1.5) and binding site (BS ≥ 0.5) scores.

For a 3 1 multivalent ligand model, three possible binding sites were considered (eqs 3– 5) 3 4 5wherepresent3 represent binding of the Ubl domain (P) to three different UIM sites (L1 L3, respectively) on ataxin-3.

We employed B. subtilis AbrB as a model protein, whose binding sites were recently determined by use of the ChAP-chip method to be >600 sites scattered across the genome.