PrimeX

PrimeX PrimeX is an advanced tool to facilitate protein crystal structure refinement and produces accurate structures more compatible with computational chemistry applications than those produced by other protein refinement programs. Traditional protein crystallography introduces issues for downstream modeling due to high-energy contacts and missing hydrogens. PrimeX addresses these concerns by restraining protein geometry to OPLS-AA, adding hydrogens during refinement, and improving nonbonded interactions for better structure accurac

 

PrimeX has some unique capabilities:

• Extended polypeptides can be built into electron density. Loops (stretches of amino acids with two anchor points) of up to 40 residues in length and tails (stretches of amino acids with one anchor point) of up to 20 residues in length can be built without manual intervention. Polypeptides are built from the target sequence, not from the sequence of the initial model.

• Multiple side chains can be placed cooperatively: the correct conformer can be found for each side chain even though they may occupy the same volume in the starting model.

• Point mutations can be performed automatically to bring the sequence of the initial model into agreement with the target sequence.

• All topology and parameter generation for ligands and modified side chains are handled automatically.

• Application of the OPLS force field for geometric restraints produces a finished structure already prepared for use with other Schrödinger computational tools.

PrimeX also has access to the wide range of structure and surface manipulation and management tools that are a part of Maestro.

PrimeX can handle up to 3000 amino acids and 5000 waters on a 64-bit machine (using the linux-x86_64 architecture).

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