Energy drift is often used as a measure of the quality of the simulation, and has been proposed as one quality metric to be routinely reported in a mass repository of molecular dynamics trajectory data analogous to the Protein Data Bank.
T7 polymerase has been crystallised in several forms and the structures placed in the PDB.
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The HH-suite comes with a number of useful databases of profile HMMs that can be searched using HHblits and HHsearch, among them a clustered version of the UniProt database, HMMs for the protein data bank of protein structures, for the Pfam database of protein family alignments, the SCOP database of structural protein domains, and many more.
The HHpred server and the HH-suite software package offer many popular, regularly updated databases, such as the Protein Data Bank, as well as the InterPro, Pfam, COG, and SCOP databases.
The PDBbind database is a comprehensive collection of experimentally measured binding affinity data (Kd, Ki, and IC50) for the protein-ligand complexes deposited in the Protein Data Bank (PDB).