days
Select Description Author Updated
Interfaces and Automation
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
06/07/2011
QSite Binding Energies : Performs a QM/MM-PBSA calculation to compute binding energies for one or more ligands from a poseviewer file.QSite ]Schrödinger
03/23/2011
Simple Interface for Surface Generation : Simple interface for the generation of molecular surfaces.Schrödinger
03/23/2011
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
03/23/2011
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
06/13/2011
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
Interactive Minimizer : This simple interface allows for rapid, interactive minimizations of the Workspace structure.MacroModel , or Prime ]Schrödinger
01/17/2011
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
01/17/2011
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
01/17/2011
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
03/23/2011
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
03/23/2011
Color by Difference : For two selected entries, colors the atoms based on their differences in the two structures.Schrödinger
01/17/2011
Delete Properties : Delete all or a set of named properties from a file and write the resulting structures out to a new file.Schrödinger
01/17/2011
Connect Disulfides : Create disulfide bonds between all pairs of cysteine residues in the workspace that have sulfur atoms closer than 3.2 Å.Schrödinger
01/17/2011
Match and Reorder Structures in One File Against a Reference Structure in Another File : Matches can be done either on a whole molecule or common fragment basis, with options to match either all the atoms or just atoms other than hydrogens in the reference structure, and to calculate the structural RMSD (after superposition). The input files can be in Maestro, SD, or PDB format.Schrödinger
01/17/2011
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
06/07/2011
Calculate Boltzmann Population : Calculate a Boltzmann population and add it as a property to the project table. This script illustrates how to manipulate project table data in Maestro and how to apply a selection filter.Schrödinger
01/17/2011
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
01/17/2011
Generate SMARTS : Create a (non-canonical) SMARTS string property for each entry in the project table.Schrödinger
01/17/2011
Generate SMILES : Create a (non-canonical) SMILES string property for each entry in the project table.Schrödinger
01/17/2011
Convert MacroModel Energies to kcal/mol : Create new versions of all MacroModel energy properties in the project table, converting them to kcal/mol.Schrödinger
01/17/2011
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
01/17/2011
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.Schrödinger
06/20/2011
Create X-Vol Ligand : A GUI for the create_xvolClash and create_xvolShell utilities found in the
$SCHRODINGER/utilities directory. Allows the user to select a hypothesis file and actives, and also specify buffer distance, grid spacing and how to compute the excluded volumes.
Phase ]Schrödinger
06/07/2011
Molecular Descriptors : A graphical user interface to compute molecular descriptors, such as topological descriptors, MOPAC properties, and QikProp properties.Schrödinger
06/07/2011
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
03/23/2011
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
03/23/2011
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
06/07/2011
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
03/23/2011
Phase Simple Hypothesis : Simple gui to generate Phase pharmacophore hypotheses and perform database searches. A subset of the most commonly used features from the Create Hypothesis and Find Matches to Hypothesis panels in Phase are exposed here.Phase ]Schrödinger
09/22/2011
Docking / Docking Post-processing
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
02/14/2012
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
06/01/2011
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
05/27/2011
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
06/07/2011
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
06/07/2011
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
06/07/2011
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
01/17/2011
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
06/07/2011
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
01/17/2011
Constrained Docking Against Multiple Cores : Iterates through a file of core positions and runs a separate Glide core-constrained docking calculation for each core.Glide ]Schrödinger
01/17/2011
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
06/07/2011
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
03/23/2011
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
06/07/2011
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
01/17/2011
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
06/07/2011
Simple Docking : A script which provides a simple interface for Glide docking.Glide ]Schrödinger
01/17/2011
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
07/13/2011
Run SiteMap on a Trajectory : Script for running SiteMap on each frame of a Desmond trajectory or on a series of structures.SiteMap ]Schrödinger
01/06/2012
Desmond Metadynamics Analysis (2011) : This script analyzes results from Desmond
Metadynamics jobs and returns free energy surface (FES) along the
reaction coordinates defined in the simulation. This script can
read both Desmond output (*-out.cfg) and free energy surface
(*.fes) files. The output can be exported as an image file.
Schrödinger
08/11/2011
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
06/17/2011
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
06/07/2011
Replica Exchange Review : A graphical interface to plot exchanges from a Desmond replica exchange molecular dynamics (REMD) simulation. The plot shows the transitions for each temperature as a function of time.Schrödinger
06/07/2011
Calculate Radius of Gyration : Calculate the radius of gyration of structures in the input file.Schrödinger
06/07/2011
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
Macrocycle conformational sampling : This script performs a combined short stochastic dynamics simulation
at high temperature with a low mode search to improve conformational
sampling of macrocycles.
MacroModel ]Schrödinger
06/17/2011
Component Interactions : This script provides a simple graphical interface that allows for the calculation of interaction energies between components of the receptor and one or more ligands. Automatic setup options allow for the calculation of either interactions between receptor residues and the ligand or ligand functional groups and the receptor.MacroModel ]Schrödinger
06/07/2011
Conformational Search and Cluster : Script to automate the process of performing a high-quality MacroModel ligand conformational search followed by clustering to reduce the output to a set of diverse conformations.MacroModel ]Schrödinger
01/17/2011
Evaluate FR Templates : Evaluates templates reported by Prime's Fold Recognition program for their suitability as templates for homology modeling.Prime ]Schrödinger
06/17/2011
Build Loops and Predict Side-chains (Single Chain) : Command-line Perl script to build missing loops and predict missing side chains using the Prime building and refinement facilities. Ligands can be included. The input is a pdb file that contains the SEQRES records. Functional for single protein chains plus any number of ligands.Prime ]Schrödinger
01/17/2011
Build Loops and Predict Side-chains (Multi-Chain) : Command-line Perl script to build missing loops and predict missing side chains using the Prime building and refinement facilities. Ligands can be included. The input is a pdb file that contains the SEQRES records. Functional for multiple protein chains plus any number of ligands.Prime ]Schrödinger
01/17/2011
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
06/07/2011
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
01/17/2011
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
03/23/2011
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
01/17/2011
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
01/17/2011
Cluster Water Molecules : Cluster water molecules from multiple structures. Based on work by Sanschagrin, PC; Kuhn, LA, Protein Sci. 1998 Oct;7(10 ):2054-64 "Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity."Schrödinger
01/17/2011
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
01/17/2011
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
01/17/2011
Average Structure : Calculate the average structure, or a most representative one, from a set of selected entries.Schrödinger
01/17/2011
Compare Ligands in Different Files : Command line script to compare two input files and write structures that either: 1) occur in both files, 2) occur only in the first input file and not the second, or 3) occur in only one of the input files. The comparison is based on either titles or SMILES strings (not canonical SMILES).Schrödinger
03/23/2011
Convert FASTA to Human Readable Text File : Script to convert FASTA sequence alignment files to a more human readable format.Schrödinger
01/17/2011
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
01/17/2011
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
01/17/2011
Search Online PDB : This script opens a panel that allows for keyword searching of the Computational Molecular Biology PDB database hosted by NIH.Schrödinger
01/17/2011
