1. Introduction

The Score service allows to calculate some different docking scores of ligand-receptor complex that can be submitted as a whole file containing both interaction partners or as two separated files. The calculation phase is provided by VEGA and consists in the evaluation of the following scores/energies:

* From Vitoli G. et al., Bioorg. Med. Chem. 18 (2010) 320-19.

"The MLP Interaction Score (MLP_InS) is computed using the atomic fragmental system proposed by Broto and Moreau and a distance function that define how the score decrease with increasing distance between interacting atoms. In detail, the equation to compute such an interaction score is reported below:

where f_a and f_b denote the lipophilicity increments for a pair of atoms and r_ab  is the distance between them. The first sum (p) concerns all ligand’s atoms and the second (m) all enzyme’s atoms. The basic assumption in the calculation of the MLP_InS, which encodes the contributions of the various intermolecular forces measured experimentally in partition coefficients, is that the score is favourable (i.e. negative) when both increments have the same sign (as denoted by the negative sign in in the equation), or unfavorable (repulsive forces) when the score has a positive sign. When the atomic parameters are both positive, MLP_InS encodes hydrophobic interactions and dispersion forces, the importance of which is well recognized in docking simulations, and it accounts for polar interactions, in particular H-bonds and electrostatic forces when the atom ic parameters are both negative".

This service allows to download the results as XML file that contains the energy contributions of each atom and residue.

2. How it works

The molecule/s sent by the user is read by VEGA that provides the following steps:

1. if you sent two separated files, VEGA creates the complex keeping the original atom coordinates, otherwise if you sent a whole file, VEGA detects the molecules and if there are more than two molecules, it will consider as ligand the molecule number indicated in the specific field;
2. atomic charges attribution (optional);
3. evaluation of the scores selected by the user.

WARNING:

• This service doesn't perform docking calculations.

• The input structures must have the hydrogens.

• For better results, submit structures optimized by a molecular mechanics software (Amber, Charmm, Gromacs, NAMD, etc).

3. Output file format

The file generated as output is in XML format and follows this scheme that highlights the meaning of each tag:

<score version="1.0">

<type id="SCORETYP" value="SCOREVAL">

    <description>
      Score description
    </description>

    <atoms number="atmnum">

      ...

    </atoms>

    <residues number="resnum">

      <residue name="resname"
       number="resnum"
       chain="cid"
       mol="molnum"
       energy="eneval"/>
      ...

    </residues>

 </type>

  ...

</score>