Sentence examples for two protein structure from inspiring English sources

In order to obtain the optimal conformations, the two protein structure models were chosen as the initial coordinates for molecular dynamic (MD) simulations with AMBER 9.0 software package.

Our study is carried out using two protein structure alignment benchmarks: Sisyphus and FSSP.

The user enters two protein structure IDs, and SMAP downloads the relevant protein structures from the RCSB Protein Data Bank (PDB) [ 18].

To obtain the tertiary structure of these proteins, we used two protein structure prediction servers FAMS [ 18, 19] and phyre2 [ 20, 21] to predict the structure using only the amino acid sequence of the protein (see Additional file 5 for the amino acid sequences (in fasta format) that were used to predict the tertiary structures of the proteins).

Vorolign compares two protein structures and produces a structural alignment of the two structures and an associated alignment score.

This server computes structural alignments between two protein structures using the DaliLite-pairwise option (version 3.1) [ 80].

Even in the absence of obvious sequence similarity, structural similarity between two protein structures can imply common ancestry, which in turn can suggest a similar function (i.e. a binding site).

The two family alignments were aligned using a structural alignment of the two protein structures.

This score has a very different property from conventional structural similarity measures: no matter how similar two protein structures are, they cannot have a high DS score unless they are in different conformational states.

Determining the optimal alignment between two protein structures, however, remains a hard problem.

Molecular centroids of two protein structures were adjusted so that they fall within 30 angstrom radius wall.