NodeConfGen

Source

Search for ligand conformations like those found in ligand-receptor complexes, with one of several validate search methods, and with optimal minimization of input and output structures.

Backend implementation

$SCHRODINGER/confgenx
Input ports
  1. Input in Maestro, Sdf or Mol2 format Type: Data
    Input in Maestro,Sdf or Mol2 format
Output ports
  1. Output in Maestro format Type: Data
    Output in Maestro format
  1. Phase Screening
    Pharmacophore Phase
    Screen a file against one hypothesis. Prepare a set of ligands and create a Phase database. Screen this database agains…
    jcmozzic > Public > Schrodinger workflow examples > Pharmacophore > Phase screening > Phase screening 1
  2. Conformational search analysis
    Molecular Mechanics ConfGen Conformations RMSD Distance Python Rotatable Bonds Conformer Clustering
    Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular dist…
    jcmozzic > Public > Schrodinger workflow examples > Molecular Mechanics > Conformational search > MM Conformational search 1-2
  3. Conformational search analysis
    Molecular mechanics ConfGen Confromations RMSD Distance Python Rotatable Bonds Conformer Clustering
    Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular dist…
    schroedinger > Public > Schrodinger_workflow_examples > Molecular Mechanics > Conformational search > MM Conformational search 1-4
  4. Conformational search analysis
    Molecular Mechanics ConfGen Conformations RMSD Distance Python Rotatable Bonds Conformer Clustering
    Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular dist…
    schroedinger > Public > Schrodinger_workflow_examples > Molecular Mechanics > Conformational search > MM Conformational search 1
  5. Phase Screening
    Pharmacophore Phase
    Screen a file against one hypothesis. Prepare a set of ligands and create a Phase database. Screen this database agains…
    schroedinger > Public > Schrodinger_workflow_examples > Pharmacophore > Phase screening > Phase screening 1-2
  6. Bioisosteres - in LiveDesign
    LiveDesign LigPrep ConfGen
    Replace functional groups of each LiveReport ligand with bioisosteres, generating all the single replacements. The work…
    schroedinger > Public > Recent_requests > LiveDesign > Bioisosteres
  7. Conformational search analysis
    Molecular Mechanics ConfGen Conformations RMSD Distance Python Rotatable Bonds Conformer Clustering
    Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular dist…
    schroedinger > Public > Schrodinger_workflow_examples > Molecular Mechanics > Conformational search > MM Conformational search 1-3
  8. Conformational search analysis
    Molecular Mechanics ConfGen Conformations RMSD Distance Python Rotatable Bonds Conformer Clustering
    Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular dist…
    schroedinger > Public > Schrodinger_workflow_examples > Molecular Mechanics > Conformational search > MM Conformational search 1-2
  9. Phase Screening
    Pharmacophore Phase
    Screen a file against one hypothesis. Prepare a set of ligands and create a Phase database. Screen this database agains…
    schroedinger > Public > Schrodinger_workflow_examples > Pharmacophore > Phase screening > Phase screening 1
  10. Phase Screening
    Pharmacophore Phase
    Screen a file against one hypothesis. Prepare a set of ligands and create a Phase database. Screen this database agains…
    schroedinger > Public > Schrodinger_workflow_examples > Pharmacophore > Phase screening > Phase screening 1-2