Sentence examples for for each pdb file from inspiring English sources

Two MD simulations were run for each pdb file.

A pocket detection algorithm called LPC (ligand protein contact) was applied to the PDB dataset to generate a set of 20,414 ligand-binding protein pockets whose coordinates were given in each PDB file under the header 'PKT', which is an abbreviation for 'pocket' [ 28].

As a result, this module generates a list of 3D patterns detected in each PDB file.

In this work, we used MED-SuMo on a fragment database derived from the PDB: each pdb file is converted into one or more pdb files containing a single fragment as ligand.

All protein structures were downloaded from the RCSB PDB database [1], and ligands denoted with the HET (heteroatom) identifier were removed from each PDB-file prior to computations.

10 Inserts were modeled using PyMOL 20 and the published coordinates for Caf1 (PDB file: 1Z9S) 10 and finally five mutants were expressed and purified.

The search retrieved a smaller set of pyrophosphatases from animal and bacterial sources, and the scores were reduced to less than half the score obtained with the Rd.HMM generated for the unmodified PDB file.

The Mathematica scripts for reading the PDB file and performing the calculations were extensively modified versions of the Mathematica notebook Inertiatensor.

Figure 3 shows part of the server output screen in which the sequence overview and the peptide scan results are shown for a sample PDB file.

For each of the pdb files that contain one to several protein chains, the chains were separated and surfaces of each chain were obtained through molecular surface calculation program, MSROLL version 3.9.3 [ 28], and then voxelized.

It includes, for each target, a pre-processed PDB file and a set of active compounds and decoys, with an average actives/decoys proportion of 2%%.