Additional Solutions available on the DiscoveryScript Library Page

Visualization

• Free DS Visualizer
• Align Molecules to a Substructure Template (DS 2.1)
• New DS Visualizer Component for Visualizing All DS File Types (CHM, MSV, etc) (DS 2.1)
• 3D Conformer/Active Site Visualization in Web Port

ADME/Tox

• Learned Model Feature Browser using TOPKAT (DS 2.1)
• Toxicity Prediction (TOPKAT) Detailed Report

Library Analysis and Design

• Find Similar Molecules by Fingerprints with Reference Name All Hits (DS 2.5.5)
• Compare Libraries Using the Minimum Percent of the Global Fingerprint (DS 2.1)
• Molecular Transformations using SMIRKS
• Database Searching and Alignment using SMARTS
• Filter Molecules using SMARTS
• Write Canonical Smiles
• Remove Salts and Remove Duplicate Molecules from a Database
• Extract Ring Structures

Pharmacophore Modeling

• Clean 1D Supplier Information from CAP Database Output (DS 2.1)
• Run Ligand Pharmacophore Mapping and Save Selected Mapped Atoms to Individual MSV files
• Run Ligand Pharmacophore Mapping and Save Selected Mapped Atoms to a Multi-Cmpd MSV file
• Prepare SD File for 3D QSAR Pharmacophore Generation
• Search Multiple 3D Databases
• Analyze Ligand Pharmacophore Mapping Results by Calculating a ROC Score
• Change Cmpd Names to a Root Name and a Numeric Suffix, Reorder by Decreasing Activ
• Analyze Conformational Models from 3rd Party Algorithm
• Analyze Conformational Modeling Building Methods using X-Ray Bound Ligands

Protein Modeling

• Run BLAST Search on a Set of Sequences (DS 2.5)
• RCSB Advanced Search in Discovery Studio (DS 2.5)
• Generate Aligned Proteins, Ligands and Fragments for a Protein Family (DS 2.1)
• Download List of PDB files and Superimpose All Structures (DS 2.1)
• Prepare Protein (Auto Complete) (DS 2.1/PP 6.1.6)
• Updated Auto Homology Modeling Protocol (DS 2.1/SES 7.0.1)
• Output Protein Structure Files after LOOPER (DS 2.1)
• Mutate Amino Acid Residues Using a DiscoveryScript component (DS 2.1)
• Process BLAST/PSI-BLAST Results by Adding the Organism Info to the Sequence Name
• Intermolecular Hydrogen Bonds for Nucleic Acid Systems (Updated for DS 2.1)
• Clean and Protonate PDB Files
• Extract Protein Poses from ZDock Output and Store in a Single MOL2 File
• Profiles-3D Verify Score calculation for processing multiple model MSV files
• Auto Loop Refinement by MODELER
• Auto Profiles-3D Verify Score Calculation Protocol For Multiple PDB Models
• Run DS MODELER with Python script

QSAR

• Retrieve Model Description of a QSAR model
• Leave-Many-Out Validation Protocol for Bayesian Model
• Create GFA Model using CSV File as Input
• Add Molecular Properties from a CSV file to a Multi-Conformer Database SD File
• Delete user built QSAR models

Receptor-Ligand Interactions

• P-Novo for Structure-based Lead Optimization (DS 2.5.5)
• E-Novo for Structure-based Lead Optimization (DS 2.5.5) (DS 1.7)
• Filter Ligands Based on HBond and Hydrophobic Protein Interactions (DS 2.1)
• Calculate Distances Between Ligand Atoms and Receptor Atoms in a Complex (DS 2.1)
• Analyze Protein-Ligand Complexes by Comparing Binding Sites (DS 2.1)
• Parallel Version of the Prepare Ligands Protocol (DS 2.1)
• Post Flexible Docking Ligand Minimization
• Export Ligands from PDB Files (updated for DS 2.1)
• Get Textual Data (Supplier Info) for LudiCAP 3D Structures
• Hydrogen Bond Interaction Filter
• Automated De Novo Workflow in DS 2.0
• Automated De Novo Workflow in DS 1.7
• Create Ligand/Protein Complex and Assign Forcefield Types (updated for DS 2.1)
• Ligand Preparation Protocol for Pipeline Pilot 5.1.2

Simulations

• Gentle Minimization Protocol (DS 2.5)
• Ligand Minimization with Implicit Solvent (DS 2.5)
• Quench (Slow Cool) Dynamics (DS 2.5)
• Correct Reimaged Solute Trajectory (DS 2.5)
• Prevent "Distortion" of a Trajectory When Using PDC Due to Reimaging (DS 2.5)
• Merge and Analyze Trajectory (DS 2.1)
• Run DMol3 Calculation from Pipeline Pilot Client (DS 2.1)
• Minimization with New Parameters to Scale Constraints (DS 2.1)
• PBC Solvation Without Reorientation of the Solute Molecule (DS 2.1)
• Dynamics (Heating and Cooling) with New Temperature Increment parameter (DS 2.1)
• Implicit Membrane Calculation Tools for DS 2.1 (GBSW)
• Heat a Small Molecule, Minimize Each Conformation, and Cluster by RMSD (DS 2.5)
• Scan Molecule Through Implicit Membrane in DS 2.0
• GBSW Implicit Membrane Protocols for Discovery Studio 2.0.x
• Binding Free Energy for a Single Complex Trajectory (updated for DS 2.5)
• Perform Standard Dynamics Cascade on a Series of Ligand Poses
• MMGBSA on Frames of MD Trajectory
• Combined Solvation and Standard Dynamics Cascade
• Minimize a Set of Conformations from a MD Trajectory
• GBSW Implicit Membrane for DS 1.7
• GBSW Implicit Membrane for DS 1.6