Glide ligand docking jobs require a set of previously calculated receptor grids and one or more ligand structures. Preparation of…

Split structures by chain, molecule, or residue. Backend implementation $SCHRODINGER/run split_structure.py

Opens 2D Sketcher Backend implementation $SCHRODINGER/utilities/2d_sketcher

Adds hydrogen atoms to produce an all-atom structure. Backend implementation utilities/applyhtreat The command line tool applyhtr…

This script performs a pairwise superposition of multiple structures using the C-alpha atoms of selected residues. The reference …

Read alignment files in FASTA and Maestro format. The input format is determined by the file extension. Note that alignments are …

Write alignments to a file in FASTA and Maestro format. The output format is determined by the file extension. Backend implementa…

Assigns double and triple bonds to input structures based on molecular geometry (bond length, bond angles, and dihedral angles). …

Generate QSAR models for a chosen property of a set of compounds, and apply the QSAR model to other compounds. Descriptor data an…

Choose structures to make predictions for and the model to apply. When the job finishes, the structures with the predicted values…

Search a protein sequence database using BLAST Note: To enable web-based searching, please ensure the option "Allow use of web se…

Tests this workflow in batch execution. Backend implementation KNIME_batch.py

Build a Bayes model from binary or continuous training data that can then be applied to other data sets. Both training set and te…

Predict the dependent variable Y for a set of structures using a previously built Bayes model and the required independent X vari…

Replace functional groups on a set of ligands with the corresponding bioisosteres, generating all single replacements. Note: In c…

Calculate a Boltzmann population for selected entries and add it as a property. This calculates the Boltzmann energy (property 'r…

Reads multiple text files, with each file having options for loading. To remove files from the list select the file and press the…

Generate molecular fingerprints Backend implementation utilities/canvasFPGen canvasFPGen is used to implement this node.

Reads Binary Canvas Fingerprints into one cell. Backend implementation fpinfo.py from bundled scripts directory (Not for general …

Write Canvas Binary Fingerprint to File