Sentence examples for partial coordinates from inspiring English sources

Starting from partial coordinates of the ribose-binding protein lacking the ligand and the 10 primary contact residues, the molecular-mechanics potential is used to redesign a ribose-binding site.

The partial coordinates of yeast ArgRS (PDB 1BS2) (Cavarelli et al., 1998) as ensemble 1 and the structure 3GDZ as ensemble 2 were used as search models for ArgRS using the program Phaser from CCP4 package (Read, 2001).

Some PDB entries provide only partial coordinates of the whole protein-DNA complex structures.

By looking at the partial coordinates (n1, n2,..., n i -1), we can use this to quickly identify those partial coordinates (n1, n2,..., n i ) that may contain fingerprints B with a Tanimoto coefficient above Smin.

An example of such a grid is illustrated in Fig. 2. By comparing the partial coordinates (n1, n2,..., n i ) of a given bucket to | A1|, | A2|,..., | A i |, where i ≤ k, it is possible to upper-bound the Tanimoto coefficient between A and every B in that bucket.

PDA can restore the full atomic coordinates of protein-DNA complex structures from partial coordinates, accurately detect DNA base-pairs with a new and simple algorithm, recognize double-stranded DNA structures, analyze protein-DNA contacts and define protein-DNA binding sites.

Assume the algorithm is visiting a partial coordinate at level i in the data structure.

The popular representation choices include (i) complete 3D coordinate information or partial coordinate information of backbone atoms, (ii) representation of various elements using their properties such as ϕ-ψ angle, solvent accessibility, etc.

In Section 3 we give details of this model's operational setup and geometry, the polyhedral mesh discretizing the spatial coordinates and the partial differential equations governing the gas flow in the oven, the combustion of hydrocarbon fuel in the burner, the reactions of the chemical species and the radiative heat transfer in the freeboard.

Let S = S 1 × S 2 × ⋯ × S n be the Cartesian product space of S 1, S 2, …, S n, and let ⪰ S be the coordinate partial order on S induced by the partial orders ⪰ i.

Because of our interest in electrostatics and high throughput ligand-based virtual screening, we sought to exploit the information contained in atomic coordinates and partial charges of a molecule.