Ligand Preparation

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.

Views

This node has no views

Workflows

• KNIME_projectKNIME Hub
• Pharmacelera_LigandPreparation_MultiServerKNIME Hub
• Pharmacelera_Standard_VSKNIME Hub
• Pharmacelera_VS_ChEMBL_SearchKNIME Hub
• Pharmacelera_VS_ROCcurveKNIME Hub

Links

• No links available

Developers