days
Select Description Author Updated
Interfaces and Automation
Final all-atom polish refinement : This script produces an all-atom model that is consistent with the
diffraction data and force field parameters, starting with an initial
refined crystal structure. It applies reciprocal-space optimization of
coordinates and thermal factors, simulated-annealing refinement, and
hydrogen-bond optimization in an automated manner. The script can generate
ionization/tautomer states for the ligands and protein. The various
optimized complexes are then assessed as to the complementarity between
the ligand and the protein using the Schrödinger docking program Glide.
The model selected as best is treated to three final cycles of automated
refinement. Click here to read the complete script description and documentation.PrimeX , Epik , Glide SP]Schrödinger
03/04/2013
Compare Ligand Files :
Compare two input files and write structure to an output file based on whether it appears in one or both files.
Schrödinger
10/01/2012
Interactive Properties :
Interactively calculates properties of interest to Medicinal Chemistry for ligands in the workspace as they are built and exports the structure and property to the Project Table.
Schrödinger
10/01/2012
Structure Morpher : Script to morph one conformation of a structure into another. This is particularly useful for generating movies from the results of Induced Fit Docking calculations, where the inputs are the initial and final structures. Movies can be made with movie.py from the Script Center or with the "Record Movie" option under the Entry menu of the Project Table.Schrödinger
10/01/2012
QSite Binding Energies : Performs a QM/MM-PBSA calculation to compute binding energies for one or more ligands from a poseviewer file.QSite ]Schrödinger
03/30/2012
Helix Manipulator . Graphical interface for manipulating phi/psi dihedral angles and positions of helices. This script was designed to greatly simplify manual refinement of GPCR homology models.Schrödinger
03/30/2012
Calpha-Calpha Distance Map :
Creates a graph of all the alpha carbon-alpha carbon (Ca-Ca) distances in a structure.
Schrödinger
03/31/2012
Planar Angle Measurement :
Measure the angle between two planes chosen by picking atoms or specifying SMARTS patterns.
Schrödinger
03/31/2012
Show Atom Properties :
Show a panel of properties for each atom the mouse hovers over.Schrödinger
03/31/2012
Visualize H-Bonds :
Visualize hydrogen bonds near selected atoms. The tool will display h-bonds and optionally label: H-bond distance, distance between the two heavy atoms, and donor/acceptor angles.Schrödinger
10/01/2012
SMARTS Index Identifier : A script to evaluate a SMARTS pattern in the workspace and identify the SMARTS atom index of selected atoms within the workspace.Schrödinger
10/01/2012
Assign GPCR Generic Numbering : This script assigns generic numbers to a GPCR structure in the Workspace using either the rhodopsin or beta-2 adrenergic receptor structures. The numbering scheme is based on the system described by Ballesteros and Weinstein (Ballesteros, J.A.; Weinstein, H., "Integrated Methods for the Construction of Three-Dimensional Models and Computational Probing of Structure-Function Relations in G-Protein Coupled Receptors," Methods Neurosci., 1995 , 25 , 366–428).Schrödinger
06/03/2011
Select Disallowed Backbone or Side Chains : A script that will analyze protein side chain or backbone torsions for the Workspace structure and select those that have chi1/chi2 or phi/psi in the 'disallowed' region. These selected residues can then be refined, for example, with Prime .Schrödinger
03/30/2012
Display Hydrophobic Interactions : A script to show hydrophobic interactions between a ligand and receptor. This is done by showing the 'good' contacts between the hydrophobic atoms of the ligand and the hydrophobic residues of the receptor. The ligand and receptor are automatically detected.Schrödinger
10/01/2012
Renumber proteins by 3D alignment : This script renumbers protein structures in the workspace based on a structural alignment. The new numbers are equivalent to the positions of the residues in the structure-based sequence alignment.Schrödinger
03/30/2012
Display Distances from Atom : Displays a panel which allows the user to specify a distance threshold and then pick an atom in the workspace. All distances between that picked atom and any other in the workspace are displayed if they are less than the threshold.Schrödinger
10/01/2012
Color by Difference : For two selected entries, colors the atoms based on their differences in the two structures.Schrödinger
03/30/2012
Delete Properties : Delete all or a set of named properties from a file and write the resulting structures out to a new file.Schrödinger
10/01/2012
Mutate Residues : This script displays a panel that allows for picking of a residue from the workspace and then selection of residues from the list. Clicking Mutate will then mutate the selected residue to each of the ones selected in the list, creating a new entry for each mutant.Schrödinger
06/15/2011
PDB Name Assignment : A python script that uses MacroModel substructure definitions to set PDB atom and residue names for a structure. This script illustrates how a single module can be used both inside and outside of Maestro .Schrödinger
03/30/2012
Calculate Boltzmann Populations :
Calculate Boltzmann populations from a chosen energy property for the selected or included entries. Units are detected and converted automatically.Schrödinger
10/01/2012
Compute Principal Moments of Inertia :
Calculate the principal moments of inertia for all selected entries in the project table. Each selected row will have the three principal axes properties added.
Schrödinger
03/31/2012
Import Structures from Project :
Allows the import of structures from one project into another project. The project imported from may be an existing project directory or the current Maestro project, and the project imported to may also be an existing project, the current Maestro project, or a new project can be created.
Schrödinger
10/01/2012
Project Table Plot :
Plot data from the Maestro project table. Multiple plots are supported, as are multiple dataset per plot and histograms. For scatter plots,the symbol color and/or size can be controlled via association with properties in the project.
Schrödinger
10/01/2012
Color by Relative Energy : Use any MacroModel relative energy to color selected entries in the project by the property. Leaves entries without this property alone.Schrödinger
03/30/2012
Generate SMARTS : Create a (non-canonical) SMARTS string property for each entry in the project table.Schrödinger
03/30/2012
Generate SMILES : Create a (non-canonical) SMILES string property for each entry in the project table.Schrödinger
03/30/2012
Convert MacroModel Energies to kcal/mol : Create new versions of all MacroModel energy properties in the project table, converting them to kcal/mol.Schrödinger
03/30/2012
Jaguar Energy Converter : For the selected entries in the project table, calculate a new property which is the relative energy in kcal/mol based on the Jaguar QM Energy in Hartree.Schrödinger
03/30/2012
Clustering of Conformers : A graphical user interface and command-line script to cluster conformations based on Cartesian or torsional RMSD. User can specify the atoms to use (based on the ASL) and the clustering settings.Canvas ]Schrödinger
01/02/2013
Molecular Descriptors : A graphical user interface to compute molecular descriptors, such as topological descriptors, MOPAC properties, and QikProp properties.Schrödinger
10/01/2012
Interaction fingerprints : Graphical interface and command-line script to compute interaction fingerprints between a receptor and ligands. Results can be visualized, sorted by similarity, and clustered. Interactive matrix shows interactions in the Workspace. Clicking cells in the clustering matrix shows 2D structures for each pair of ligands. Results can be incorporated into the Project Table.Canvas ]Schrödinger
10/01/2012
Spectral clustering : A script that implements the Spectral Clustering method as described by Mark Brewer in 'Development of a Spectral Clustering Method for the Analysis of Molecular Data Sets,' J. Chem. Inf. Model , 2007 , 47 , 1727-1733. The cluster properties (cluster membership, cluster contribution and cluster eigenvalue) are added to the project table for each input entry.Canvas ]Schrödinger
03/30/2012
Cluster Molecules by Fingerprints : Cluster molecules by fingerprints using Canvas . Users can select the fingerprint type, similarity metric, and linkage method. Can also be used to compute similarity of selected entries to Workspace entries.Canvas ]Schrödinger
03/30/2012
Cluster Based on Volume Overlap : Generates a matrix of volume overlaps between user-specified molecules followed by hierarchical clustering. The clusters are output to the Project Table.Schrödinger
03/19/2013
Create Phase Databases :
For each structure file in a specified directory, create a Phase
database under a user-defined absolute path.
Phase ]Schrödinger
03/31/2012
Docking / Docking Post-processing
Calculate Entropy :
Calculate the entropy and Boltzmann-weighted energy (in kJ/mol) for a multi-entry file. The temperature (in K) can be adjusted and the relative energy property can be specified.
Schrödinger
03/31/2012
Glide Ligand Designer :
Tools for designing a ligand in the context of a receptor. It provides display tools and access to Glide scoring for the interaction energy of the ligand with the receptor.
Glide Elements]Schrödinger
10/01/2012
Lead Optimization Docking :
Edit a structure that is docked to a receptor, and dock the edited structure. Allows checking the effect of structural modifications to a ligand on the docking score.
Glide ]Schrödinger
10/01/2012
Compare Ligand Ranks :
Compare ranks of compounds in structure files that are ordered in ascending rank (best first). The output is a csv file with the sum of the observed ranks, the individual rank observations, the name of the input file from which they are observed, and (optionally) RMSD comparisions.
Schrödinger
03/31/2012
Split Structure by Substructure :
Split structures by chain, molecule, residue, ligand or pdb. Mode=pdb will split the structure into 1) receptor, 2) each individual ligand, 3) all non-metal ions and cofactors, 4) all waters.
Schrödinger
10/01/2012
Compute Ligand Volume :
Compute the volume for each ligand or active site in a file. In ligand mode, the volume of the entire structure is calculated. In active site mode, the unoccupied volume within a cube is calculated.
Schrödinger
03/31/2012
Find receptor-ligand interactions : Detect interactions
between a receptor and a set of ligands in a poseviewer file. The
script lists each H-bond and contact (good, bad, or ugly) along with
a summary reporting the number of ligands forming each kind of
interaction with each receptor residue. The script also detects hydrophobic, salt-bridge, pi-cation, and pi-pi interactions.Schrödinger
03/30/2012
Block-sort Glide Results : A command-line script for block-sorting Glide results, in which the results for each ligand are grouped and sorted by Emodel (HTVS/SP) or the XP poserank, and then the ligand blocks are sorted according to the GlideScore of the top member. The property that identifies a ligand (for grouping its poses) can be specified by the user; the default is to use the structure title.Schrödinger
06/17/2011
Compute SASA of ligands in a complex : A command-line script to estimate the Solvent Accessible Surface Area of a ligand or pose in the context of a receptor.Schrödinger
03/30/2012
Pose Explorer : This script can use pre-existing properties such as Glide descriptors or it can compute Canvas 2D Fingerprints, Interaction Fingerprints and Molecular Descriptors. It then clusters compounds based on those properties using Canvas Self-Organizing Maps. Properties can then be projected onto these maps to find how property values differ between clusters. Clusters on different maps can also be compared to find sets of properties that differentiate similar compounds.
Canvas ]Schrödinger
10/01/2012
Binding SASA : Script to compute the change in solvent accessible surface area (SASA) upon binding for a ligand and receptor. The total SASA for the unbound system and the difference upon binding is computed and decomposed into functional subsets, such as per-residue terms, charged, polar, and hydrophobic.Schrödinger
03/30/2012
Glide Cross Docking : Graphical interface and command line tool to automate cross docking calculations with Glide. Options allow for the automatic preparation of ligand and protein, cross docking using ligands from complexes and/or an external ligand file, and analysis of the results.Glide ]Schrödinger
10/01/2012
Enrichment Calculator : This script computes enrichment metrics from virtual screening calculations using the output structure file and a list of known actives. The metrics include standard enrichment factors (EF), area under the receiver-operating characteristic curve (AUC), robust initial enhancement (RIE), and Boltzmann-Enhanced Discrimination of Receiver-Operating Characteristic (BEDROC).Schrödinger
03/30/2012
XP Atom Energies : This script adds Glide XP terms from .xpdes file to a Maestro file as atom-level properties. These properties can be used to color and visualize atoms by the values.Schrödinger
10/01/2012
E-Pharmacophores : This script extracts the energetic descriptors of the Glide XP score and assigns them to pharmacophore features. The resulting energy pharmacophore (e-pharmacophore) hypotheses can be used directly in a Phase search or can be manually modified based on visualization and the energetics. Input can be a single molecule or multiple docked fragments that result
from running Glide XP with the option to write XP descriptors (requires XP
Visualizer license). The work is based on
Salam et al., "Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis", J. Chem. Inf. Model., 2009 and
Loving et al., "Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation", J. Comp. Aided Mol.
Des., 2009. This script replaces xpdes_score_phase_hypothesis_gui.py.Phase ]Schrödinger
03/30/2012
Select Top Poses : Graphical user interface for running Glide docking jobs. User can define number of structures per compound to keep, total number of structures to report, unique property, property on which to sort.Glide ]Schrödinger
10/01/2012
Compute Extendedness of Conformations : A script to calculate the degree of extension for a collection of conformers based on the work of Perola and Charifson: "Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding", J. Med. Chem. , 2004 , 47 , 2499-2510. The degree of extension is sometimes used to qualify conformers that are likely to resemble docked conformations.Schrödinger
03/30/2012
Create or Convert Pose Viewer Files : This script can convert pose viewer files into a series of complexes, and convert complexes into ligand-only, receptor-only, or pose viewer files.Schrödinger
03/30/2012
One Step Glide Docking : Simple gui to setup and run Glide calculations in a single step. The script first generates Glide grids and then performs Glide docking. While there are only limited options available, it is possible to specify hydrogen bond constraints.Glide ]Schrödinger
03/30/2012
Compute Entropy Associated with Each Energy Well : A command line script to compute a modified docking score based on work by A.M. Ruvinsky using the number of poses within each energy well. Poses are first clustered and then the entropy is computed for each cluster. Input poses should come from Glide saving 100 poses per ligand. The criteria for duplicate pose elimination should be reduced to zero (in the Clustering section under Advanced options in the Output tab of the Glide Docking panel) in order to ensure a full sampling of each energy well.Schrödinger
03/30/2012
Pose Filter : Filters poses from a pose viewer file based on user-defined receptor contacts/interactions. The receptor atoms used in the filtering are defined by a user-specified ASL expression. The user can choose which combination of ligand interactions should be used to define a contact (for example distance, H-bond, whether the contact is in a ring or aromatic ring).Schrödinger
06/07/2011
RRHO Entropy : This script runs a MacroModel Rigid Rotor Harmonic Oscillator (RRHO) calculation on each ligand in a poseviewer file to obtain the change in translational, rotational, vibrational, and total entropy of the ligand upon binding. The output is a csv file or a Maestro file with the entropy properties.MacroModel ]Schrödinger
03/30/2012
Strain Rescore : A graphical user interface and command-line script that calculates penalties for poses with internal strain. For each ligand pose in the input file, a tightly constrained minimization and an unconstrained minimization are performed with MacroModel . The energy difference is used to determine the Glide gscore penalty. The input file can be either a 'pv.mae' file, with a receptor as the first structure, or a 'lib.mae' file that contains only ligand poses.MacroModel ]Schrödinger
10/01/2012
Binding Surface Area Analysis :
Compute before and after binding solvent-accessible surface areas for a receptor and ligand pair.
Schrödinger
10/01/2012
Monitor the Distance Between Two Atom Groups :
This script monitors the number of molecules that match a given pattern
within the given distance of a second set of atoms. The data is collected over
each frame of the trajectory and written one line per frame to a .csv file.
Schrödinger
10/01/2012
Analyze H-Bonds Over Trajectory :
Record the number of hydrogen bonds in each frame of a trajectory.
Schrödinger
10/01/2012
Atomic Fluctuations :
Calculates the atomic fluctuations of the selected atoms over a desmond trajectory.
Schrödinger
03/31/2012
Average Trajectory Structure :
Obtain the average structure over a Desmond trajectory.
Schrödinger
10/01/2012
Trajectory Covariance Matrix :
Calculate covariance matrix over a Desmond trajectory. Before the calculation, the trajectory is superimposed to an average structure which is calculated iteratively from the trajectory. Outputs the average structure and a .csv file containing the covariance matrix.
Schrödinger
10/01/2012
Measure Dihedral Over Trajectory :
Measure phi, psi, chi1 or chi2 for selected residues over a Desmond trajectory.
Schrödinger
10/01/2012
Run SiteMap on a Trajectory : Script for running SiteMap on each frame of a Desmond trajectory or on a series of structures.SiteMap ]Schrödinger
01/02/2013
Fix Corrupted Desmond Trajectory : A script to fix a corrupted Desmond trajectory. It can also create a new trajectory from all available frames if the target trajectory name is provided. A structure file is needed if the metadata file is missing or corrupted for certain kinds of Desmond trajectory formats.Schrödinger
10/01/2012
Delete Waters from Trajectory : A command line script to delete waters from a Desmond molecular dynamics trajectory. There is an option to retain the clostest N waters to the protein and ligand. Deleting waters can considerably reduce the trajectory size.Schrödinger
10/01/2012
Calculate Radius of Gyration : Calculate the radius of gyration of structures in the input file.Schrödinger
10/01/2012
Desmond Trajectory Clustering : A graphical user interface or command line script to perform hierarchical clustering on structures from a Desmond trajectory based on the RMSD matrix of a specified set of atoms.Phase ]Schrödinger
03/23/2011
Combine Fragments : Combine fragments either through direct joining or linking. Fragments must be in the same 3D frame of reference, for example, from a docking fragment calculation or from running fragment_molecule.py on docked molecules. For linking, a linker library must be provided.Schrödinger
10/01/2012
BREED : Implementation of the BREED algorithm. Molecules in the same frame of reference (i.e. from superimposed crystal structures or docked ligands) are analyzed for overlapping bonds and hybridized to make new molecules. This was developed at Vertex and first published in J. Med. Chem. 2004 , Vol 47 , No 11 "Novel Inhibitors through Hybridization of Known Ligands."Schrödinger
03/30/2012
Break Molecules into Fragments : This script will break up a set of input molecules into fragments based on some simple rules. If the input is a set of docked poses or ligands from superimposed crystal structures, then the output from this script can be used with fragment_join.py to make new molecules that swap functional groups from other molecules in the active site.Schrödinger
03/30/2012
Score and Filter Docked Fragment Poses from Glide : This script takes a Glide poseviewer file as input and outputs the top poses based on a ligand efficiency metric and spatial diversity. For ligand efficiency, the Glidescore is modified based on the number of heavy atoms. By default, we use a natural log ligand efficiency. For spatial diversity, the script takes the top poses by score for each region of the active site.Schrödinger
03/30/2012
Delete Atoms From a Structure :
Delete atoms from a structure file based on a Maestro ASL expression.
Schrödinger
10/01/2012
Remove Salts and Solvents From SMILES :
Remove common salts and solvents from SMILES strings.Canvas ]Schrödinger
03/31/2012
Measure Distance From SMARTS to Atoms :
Measure the distance between a set of ligand atoms defined by a SMARTS pattern and either a single receptor atom or a set of receptor atoms defined by an ASL pattern.
Schrödinger
03/31/2012
Documentation and Script Browser :
Access help documentation all in one panel outside of Maestro. This script also allows the searching of all python scripts in the distribution for a string and provides easy view of the scripts the string is found in.
Schrödinger
03/31/2012
Search PDB Headers :
Search the Prime PDB header database and import results into Maestro.
Prime ]Schrödinger
03/31/2012
Build Extended Peptide from Sequence :
Build one or more peptides from single-letter amino acid codes in a text file.
Prime ]Schrödinger
10/01/2012
Build Peptide with Phi/Psi Angles :
Build a single peptide with specified phi/psi angles and refine the structure with Prime. The input file should have a sequence on the first line and following lines with comma-separated phi/psi values. Prime side-chain prediction is run before returning the final the structure.
Prime ]Schrödinger
03/31/2012
Compute Centroid Distances :
Calculate the distances between the centroids of rings in a structure for many conformations of a given structure. The output file contains the ring group information as well as the inter-ring distances for each structure.
Schrödinger
03/31/2012
Structure File Converter :
Graphical interface to convert structure files between various formats.
Schrödinger
10/01/2012
Per-residue RMSD : Calculate the RMSD for each residue of 2 identical proteins. Output is a csv file with the RMSD values.Schrödinger
06/25/2011
Distribute Jobs : An application for distributing a set of serial jobs to the desired host(s) using Job Control.Schrödinger
06/17/2011
Generate Helices : Create helical structures based on one or more sequences given in a file.Schrödinger
10/01/2012
Compute Active Site Residue Identity and Homology : This script takes a set of aligned proteins and computes the residue identity and homology between the active sites of each structure. The input structures must be aligned, for example using the Schrödinger Protein Structure Alignment (structalign) program.Schrödinger
03/30/2012
Command Line RMSD Calculation : Script to Calculate the RMSD and maximum atom displacement between a pair of files. Options allow ASL selections and the ability to do either inplace or mobile RMSD.Schrödinger
06/07/2011
Rotate All : Command-line script to rotate all structures into a new reference frame. The program initially aligns the first entry from the second file onto the first entry from the first file by running the structalign program and then applies the rotation matrix to all subsequent entries in the second file. [Requires: Prime ].Schrödinger
03/30/2012
Average Structure : Calculate the average structure, or a most representative one, from a set of selected entries.Schrödinger
03/30/2012
Merge CSV Properties into a Maestro File : Command-line script to merge properties from a csv file into a structure file. A new Maestro file is generated as the output. The structure file may be mae, sdf or pdb format. The structures can either be in a poseviewer file (protein + ligands) or a library file (all ligands).Schrödinger
03/30/2012
Create Movies : Python script with functions to create movies by either rocking the current structure in the workspace or animating the selected entries. Note, this script requires that ImageMagick be installed.Schrödinger
10/01/2012
Spin Workspace :
Spin - rotate the workspace by 360 degrees around the X, Y or Z axes.
Schrödinger
10/01/2012
