Abstract
BackgroundKnowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.ResultsOur new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the PDB format can be uploaded as input. The results will be returned to the user's email address.ConclusionsOur Potentials 'R'Us server is an easily accessible, freely available tool with a web interface that collects all existing and future protein coarse-grained potentials and computes energies of multiple structural models.
Highlights
Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes
The basic idea of protein threading is that the target sequence for which the structure is being predicted is threaded through the backbones of a collection of template protein structures and energy scores are calculated for each sequence-structure alignment using knowledge-based coarse-grained potentials such as four-body potentials [3], two-body potentials [4,5] and short-range potentials [6] employed in this server
Since the short-range potentials and four-body potentials were derived in a completely different way compared from pairwise potentials, we can not calculate the Pearson correlation for them
Summary
The Pearson correlation between four-body potentials and general four-body potentials is 0.62 (Figure 2). The server will not compute energies either for NMR structures or for PDB files having more than 25000 atoms, and will only send warning messages via email. The results returned by the server via e-mail show that the native structure has the energy lower than any other decoy when threaded for all potentials except TS, MJ1, and MSBM. We have tested the potential server on a much larger set of 1783 PDB files for a protein composed of 101 amino acids; in this case it took the server around 9 minutes to compute the results and return them by e-mail. This shows that the server has the ability to compute a large number of pdb files at one time It should be convenient for users requiring energies to be calculated for large numbers of computer generated conformations. Users are encouraged to contact the system administrator via the e-mail provided on the web page to solve any possible problems or to suggest improvements to the functionality and performance of the server
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