Other molecular modeling software may also support the Mol2įormat. Some common errors in atom typing and bond typing but certainly cannot handle all the possible The bond type assignments are correct according to the Tripos force fieldĬonventions. Ligands to be stored in the SYBYL Mol2 format. It can only calculate theīinding affinities for given protein-ligand complexes. Molecules must be pre-docked into the binding pocket of the target protein. The primary thing that should be kept in mind is: the ligand How to prepare the ligands in Mol2 format? This modification will not affect X-Score's computation. To the protein, you need to remove that bond to keep the cofactor as a separate (4) If the cofactor is originally covalently bound (3) This cofactor molecule should share the same coordinate system with Note that: (1) Atom types and bond types in this molecule should be assignedĬorrectly according to SYBYL's definition. This kind of cofactors are usually not formed byĪny standard building blocks, the PDB format is not proper for presenting them.īut for instead, you can save the cofactor in SYBYL MOL2 format and specify itsĬOFACTOR_MOL2_FILE parameter in the input file. Provide such an option: it will treat the cofactor as part of the protein. Place when evaluating binding affinities of the ligand molecules. Ligand molecule inside the binding pocket, such as CoA, NADH, and etc., and maybe you want to keep it at its Sometimes there are an organic cofactor binding together with the Specifies the path and the name of this file. The parameter RECEPTOR_PDB_FILE in the input file (5) Occasionally, there are some non-natural residues on the protein, X-Score will neglect them if it cannotįind appropriate parameters for them in the parameter libraries. This happens, you may want to manually add a line for the metal to the PDB file. Them, such as SYBYL v6.8, are even unable to export metals to a PDB file. Please be cautious because not every software writes standard PDB file! Some of The PDB convention, a metal ion should be described by a line started by "HETATM". X-Score considers this kind of metal ions in computation. (4) If a metal ionĮxists inside the binding site and is believed to be important for ligandīinding, keep it as part of the protein. When preparing this PDB file, please remember: (1) Add polar hydrogen atoms.Īdd all hydrogen atoms will not hurt but only polar hydrogen atoms are needed in computation. Structure of the protein is supposed to be stored in the PDBįormat. While docking the ligand(s), for the sake of efficient computing, X-Score requires the protein and the ligand(s) Since most today's molecular docking programs will keep the protein rigid Structure could be either experimentally determined or modeled by a docking Structure of the protein-ligand complex to calculate its binding constant. How to prepare the protein in PDB format? All the parameters needed to run X-Score are assembled in an input file (click here to view anįile will be explained in detail below. Is required to be stored in a PDB file, and the ligand molecule(s) should be stored in a Sybyl/Mol2įile. Of a given ligand molecule (or multiple ligand molecules) to a target protein. The basic function of X-Score is to compute the binding score
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