Additional Solutions available on the Discovery Studio Component Library Page

Visualization

• Free DS Visualizer
• List All Bond Angle Monitors in a Molecule (DS 2.5.5)
• List All Torsion Angle Monitors in a Molecule (DS 2.5.5)
• Water Renumbering (DS 2.5.5)
• Movies and Animations from Discovery Studio (DS 2.5.5)
• Updated Create Surface Around Ligand Script (DS 2.5.5)
• Sample Use of Selecting Atoms Based on Pre-defined Groups (DS 2.5)
• Rock the View (DS 2.5)
• Tips When Using SelectByProperty (DS 2.1)
• Annotate Atom and Bond Labels with Different Fonts (DS 2.1)
• Color Series of Selected Atoms by User Specifed Color (DS 2.1)
• Color Carbon Atoms in Green for Selected Object (DS 2.1)
• Modify Color and Ball Size by Atomic Property (DS 2.1)
• Save DS Selections From Multi-Compound SD File
• Save DS Selections From all SD Files in a Folder
• Color By Molecule
• View at Specified Angle
• Export Molecules in MSV file as Multiple PDB Files
• Load Molecule at Specified Orientation
• Remove a Cell

Library Analysis and Design

• Add IC50 Values from a CSV file to Ligands in an SD or SDF File
• Convert All Primary and Secondary amines in a SD file to Tertiary Amines

Pharmacophore Modeling

• Calculate Angle Between Two Planes (DS 2.5.5)
• Calculate Minimum Distance from Centroid to a Plane (DS 2.5.5)
• Calculate Minimum Distance from Atom to a Plane (DS 2.5.5)
• Create Plane Monitors from a Set of Selected Atoms (DS 2.5.5)
• Create Excluded Spheres Query by using Protein Binding Site (DS 2.5)
• Create Ligand Pharmacophore Points based on the Defined Protein Interactions (DS 2.1)
• Create Shape Feature (One per Ligand) and Save to CHM File (DS 2.1)
• Select Mapped Atoms From Ligand Pharmacophore Mapping in 3D Window
• Create Catalyst Shape Query from Protein Cavity (Updated for DS 2.1)
• Add Exclusion Features From Bumps

Protein Modeling

• Extend Selection to Aligned Residues in Sequence Window (DS 2.5.5)
• Find Salt Bridges (DS 2.5)
• Add Phi Psi Dihedral Restraints to All Amino Acid Residues in a Protein (DS 2.5)
• Estimate Per Residue Contact Surface Area at Interface and Calculate Per Residue Int Energies (DS 2.5)
• Report the list of contact residues at the interface between two chains in a protein complex (DS 2.5)
• Build Multiple Peptides from Sequences (DS 2.5)
• Generate Multiple Mutants at Three Specified Sites Based on User Specified Lists (DS 2.5)
• RDOCK Save Multiple Molecules in One Window to Separate PDB Files (DS 2.1 or higher)
• Calculate the Change of SASA Upon the Formation of Mutiple Chain Protein Complexes (DS 2.1)
• Rename and Renumber Chains (DS 2.1)
• Analysis of ZDOCK Poses: Calculate Change of SASA upon Protein Complexation (DS 2.1)
• Generate List of Mainchain Torsion Violations and Estimate Percent Violation (DS 2.1)
• Filter Loop Refinement According to Main Chain Violations in Proposed Loop Confs (DS 2.1)
• Perform Manual Homology Modeling (DS 2.1)
• Calculating Average Structure from Many NMR Ensemble Structures (DS 2.1)
• Evaluation of the Change of SASA upon Protein-Protein Complex Formation (DS 2.1)
• List Ranges and Create Group Definitions for Protein Secondary Structures (DS 2.1)
• Post-Processing Looper Results - Extract Full Coordinates (DS 2.1)
• Construct a Single 3D Amino Acid with Interactive Changes to Protein Internals (DS 2.1)
• Highlight Interface Hydrogen Bond Residues in a Protein Complex
• Analyze Hydrogen Bonding (DS 2.1)
• Calculate Sidechain RMSD values for Loop Refinement Results
• Remove Waters from Hydrophobic Cavities on a Protein (Updated for DS 2.5)
• Color Calpha Atoms a Unique Color Based on Their Molecule Name and/or Chain Name
• Batch Process SASA Calculation for All PDB Files in a Directory (DS 2.1)
• Create Groups for Each Helix in a Protein (Updated for DS 2.1)
• Process All Files in a Specified Directory and Add Hydrogens
• List Chain ID and Residue Name of Each Selected Residue (Updated for DS 2.1)
• Calculate RMSD between Any Two Sets of Atoms Defined as Groups (DS 2.5)
• Analyze Amino Acid Contents of a Series of PDB (protein databank) or MSV files
• Create Intersection of Atom-Level Groups
• Create Missing Disulfide Bridges
• Create Groups of Specified Residues
• ZDOCK Analysis - List All Interfacing Residues Per Pose (Updated for DS 2.1)
• ZDOCK Analysis - Find Poses with Specified Residues in the Binding Interface
• Extract Protein Internals
• Analyze Multiple Models from Build Homology Models Job (Updated for DS 2.1)

Receptor-Ligand Interactions

• Color Binding Site Object by Electrostatic Potential Grid (DS 2.5)
• Nice Rendering of Protein Ligand Interactions (DS 2.1)
• Create Query From Core (DS 2.1)
• Find Binding Site and List Volumes (DS 2.1)
• Calculate Hotspot Map for LibDock
• Create SD Files for Input to the De Novo "Link" Library Generation Protocol
• Changing the Display to Highlight Protein-Ligand Hydrogen Bonds (Updated for DS 2.1)
• Create a Surface at the Ligand Binding Site

Simulation with CHARMm

• Add Fragments to Conformations of a Trajectory (DS 2.5.5)
• Fix Charges for Simulations (DS 2.5)
• Harmonic Restraints from Temperature Factors (DS 2.5)
• Convert PDB Input for Use with Standalone CHARMm
• Merge Multiple CHARMm Trajectory DCD Files into a Single DCD File (DS 2.1)
• Prepend a New Conformation to a Trajectory (DS 2.1)
• Residue based Secondary Structure List for All Frames of a Trajectory (DS 2.1)
• Tally Secondary Structure Elements of Each Conformation in a Trajectory (DS 2.1)
• Load Distance and Dihedral Constraints from a File (DS 2.1)
• Calculate the Solvent Accessible Surface Area of Selected Atoms Over a Trajectory (DS 2.1)
• Check Charges: Calculate Total Partial, Total Formal Charge, Charge Difference by Residue (DS 2.5)
• Convert Multiple Molecules into a 'Trajectory'
• Display periodic boundary conditions or print box size given msv or mol2 file
• Calculate the X, Y and Z extents of a Molecule