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The Protein Residue Distance & Angle Distribution Database for Secondary Structures (PRDDs) is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level distances and angles (called virtual bonds, bond angles, and torsion angles) obtained from their distributions in databases...
The development of an integrated software environment for protein structure refinement is reported. Energy minimization is combined with geometric embedding in the refinement program. The energy minimization procedure is used to sample the conformational space and find a group of low energy structures for further improvement. The geometric embedding is then applied to the structures with a set of...
PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level "virtual" bond and torsion angles obtained from their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying...
Computational simulations of the conversion from the normal cellular prion (PrPc) to the scrapie prion (PrPSc) are usually based on the structures determined by NMR because of the difficulties in crystallizing prion protein. Due to insufficient experimental restraints, a biologically critical loop region in PrPc (residues 167-171), which is a potential binding site for Protein X, is under-determined...
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