0 ×

Ligand Preparation

Pharmacelera Extension for KNIME Workbench version 1.0.0.v202004161715 by Pharmacelera

The ligand preparation module enables you to prepare the input file to be used by PharmScreen by minimizing the input structures, generating a set of conformations for each of them or calculating molecule parameters such as partial charges or atomic contributions to LogP.

Options

License file

Use this option to select the license file. To run the Ligand Preparation Node is necessary to have a valid license file to allow you to run simulations. To obtain a valid license file, please, contact Pharmacelera (contact@pharmacelera.com).

Minimize structure

If you are providing 2D structures in the input file it is encouraged that you minimize them if you are not going to generate conformations. In order to do so, four forcefields are available UFF, MMFF94s, AM1 and RM1.

  • UFF
    Molecular mechanics forcefield estimated using general rules based only on the element, its hybridization, and its connectivity.
  • MMFF94s
    "Static" variant of the MMFF94 forcefield, which is characterized by a different parameterization of torsional and out-of-plane interactions geared towards geometry optimization studies.
  • AM1
    A semi-empirical method for the quantum calculation of molecular electronic structure. It is based on the Neglect of Differential Diatomic Overlap integral approximation. Specifically, it is a generalization of the modified neglect of differential diatomic overlap approximation.
  • RM1
    A reparameterization of the AM1 model that improves the semiempirical molecular orbital models. It uses the same algorithms of AM1 but C, H, N, O, P, S, F, Cl, Br, and I atom parameters have been changed.
Generate conformations

Conformer generation is necessary to maximize the chemical space exploration and to consider molecular flexibility as PharmScreen operates with rigid structures. Conformations can be calculated with other external tools and provided in the input file with the same molecule name for all conformations or generated in this section with the option Generate. Conformers are generated using a distance geometry algorithm. With the default settings the number of conformers changes for each molecule depending on the number of rotatable bonds it has. Also, only those conformers with a minimum RMSD difference of 0.5 Å and a maximum energy value of 6.0 kcal/mol over the most stable conformation are kept.

Molecular charges

This section enables setting the desired method for calculating partial charges. By default, PharmScreen assumes that charges are not used. Charges are required if the Electrostatic field is selected. If you click in this section, you will see the following options: In case of using partial charges select a method to compute them. The options are: Provided in the input file, Gasteiger, Mulliken (AM1), and Electrostatic (RM1). If you have the charges in your input file select a Provided in the input file option, otherwise select the desired charge.

LogP

This section enables calculating atomic level contributions to LogP. By default, PharmScreen assumes that logP values are not used. LogP values are required if Hydro Total, Hydro Electrostatic, Hydro Cavitation or Hydro Van der Waals fields are used.

  • Provided in the input file
    Use this option when the logP parameters has been precalculated and are included in the input file.
  • MST model
    Quantum Mechanical parameters are derived from semi-empirical (RM1) IEF/PCM-MST solvation models, and are the highest quality descriptors available, although they require more computation time.
  • Atom type
    Fast parameters are a simpler model based on ALogP atom types and parametrized with custom values derived from Quantum Mechanical calculations. These parameters are significantly faster but do not take into account molecule conformations or atom types that have not been parametrized.
Number of threads

This option is used to select the number of threads used in the execution of the Ligand Preparation node.

Log file name

This option is used to indicate the path of the output log file.

SSH Configuration

Remote execution

Host

Address of the host.

Port

Port of the service.

Authentication

Method of authentication.

  • Password
    Use username and password to authenticate.
  • Keyfile
    Use keyfile to authenticate.
User

Name of the user.

Password

Password of the user, if authentication via password is selected.

Keyfile

Location of the keyfile. Note that the key file has to be in OpenSSH key file format.

Timeout

Specify the timeout for the connection in milliseconds here.

Test connection

Open dialog that test the current connection.

Input Ports

Icon
The molecule library to be processed.

Output Ports

Icon
Table with the read molecules.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Pharmacelera Extensions from the following update site:

KNIME 4.3

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.