DSC-11424

A new Screen Best Only parameter has been added to the Screen Library protocol to allow only the highest fitting pharmacophore for each compound to be reported. This option can be useful when screening a large number of ligands.

DSC-22432

The Interaction Pharmacophore Generation protocol now supports nucleic acids.

DSC-26026

The conformation generation components now sample all isomers of unknown chiral centers by default for the BEST, FAST, and CAESAR methods. Protocols that benefit from enumerating isomers such as docking will use the new default.

DSC-30908

A new Maximum Omitted Features/Option parameter has been added to the Ligand Profiler protocol to choose between maximizing the number of features or maximizing the pharmacophore fit when selecting the best fit.

DSC-31042

The Calculate Protein Formulation Properties protocol now creates aggregation sites and surfaces that can be analyzed using the View Aggregation Sites tools in the Discovery Studio Client. Additionally, Site groups are created for positively and negatively charged areas in the Charge Map.

DSC-32385

The Interaction Pharmacophore Generation protocol can now build pharmacophores from a receptor-ligand complex that has more than 50 non-bond interactions.

DSC-32389

Information on how to view examples of JSON queries after running an RCSB Advanced Search from https://search.rcsb.org has been added to the help for the RCSB JSON parameter of the RCSB Structure Search protocol.

DSC-32697

Removed benign Perl warning messages reported in the scisvr_stderr.log file.

DSC-33112 DSC-33136

Protocols that produce sortable tables in the report now work without an active server (for example: Find Activity Cliffs using MMPs, Calculate Protein Formulation, Predict Humanizing Mutations).

Note: The per-residue detailed reports in the Predict Humanization protocol are now displayed as links to separate reports.

DSC-33253

The RCSB Structure Search protocol was updated to include new substructure ligand search options recently made available by RCSB PDB.

DSC-33289

Updated the Calculate Mutation Energy (Binding) and Calculate Mutation Energy (Stability) protocols to run in pH-dependent mode by default.

DSC-33299

Enhanced the Set Up Relative FEP Calculations protocol so that FEP dual topologies can be generated for molecules that have small partial charge differences.

DSC-33339

Updated the Analog Conformation Generator component to include:

¡   Sorting conformations by protein bump scores

¡   Refinement using CDOCKER

¡   Component parallelization for efficiency

DSC-33410

Updated the Build Homology Model parameter help to correct the loop length limit for the Refine Loops parameter.

DSC-33415

Enhanced the Assign Forcefield protocol to correctly assign customized nucleotide templates.

DSC-33481

Discovery Studio 2022 is built on Pipeline Pilot 2022.

DSC-33486

Added new scripting APIs to calculate protein molecular and residue properties. These include: SetResidueOneHotVectors, SetBlackAndMouldHydrophobicities, CalculateFractionalResidueExposures, CalculateProtrusionIndices, CalculateDepthIndices, CalculateElectrostaticPotentials, and CalculateResidueNeighborhoodFeatures. Also added FindSurfacePropertySites, which clusters certain surface residues into groups depending on their property values.

DSC-33506

Enhanced the Align Sequences protocol to allow long sequence names.

DSC-33519

The Discovery Studio client Jobs Explorer is now available without a server connection.

DSC-33523

The MSLD Ligand Generator component can now generate multi-topology systems when input ligands have small differences in partial charges.

DSC-33524

The Set Up MSLD calculations protocol can now generate multi-topology systems when input ligands have small differences in partial charges by changing the Partial Charge Tolerance parameter.

DSC-33528

The Calculate Energy (QM-MM) protocol now uses the Intel MPI libraries from the mpiruntime package.

DSC-33540

The scheme (http/https) was removed from the Jobs Explorer Server Location column to standardize server names.

DSC-33553

The MolecularOverlay scripting API was enhanced to allow for the calculation of RMSD and similarity properties without alignment (based on the original atomic coordinates).

DSC-33564

The Mol2 file reader and writer (used in simulation protocols) now use less memory when handling large solvated systems.

DSC-33574

Updated SQLite to 3.35.2.

DSC-33581

Parameters in the Parameters Explorer are now automatically updated in the Discovery Studio Client when switching servers. This can be helpful when different protocol versions exist on the servers.

DSC-33599

Added two new components, Build Antibody Framework Models and Refine Antibody CDR Loops. Also, added parallel processing parameters to the Graft Fabs onto Full Length Antibody component.

DSC-33652

Qt for the Windows version of Discovery Studio is upgraded to 5.15.

DSC-33688

Enhanced the Protein Preparation component with parallel processing options and used the latest component in the Prepare Protein protocol.

DSC-33693

Added a new component, Calculate Protein Features, which calculates a variety of structure-based descriptors at the molecule and residue levels. These features may be useful for machine learning applications.

Added a utility component, Extract Residue Properties, which extracts residue properties from a macromolecule, creating a generic record per residue.

DSC-33739

Discovery Studio 2022 is now compatible with the CCDC GOLD 2021.

DSC‑33773 DSC-33695

A new protocol, Predict Excipient Interactions, allows you to use a machine learning method to predict preferential interaction coefficients for a range of common excipients. This allows for a qualitative assessment of areas of relative inclusion or exclusion of excipients on an antibody surface.

DSC-33784

A new site was added to the default URL Location preferences to provide access to the AlphaFold Protein Structure Database via the Open URL dialog. It should be noted that these are theoretical predictions based on proteome sequences, and may therefore not represent biologically active entities.

Note: The new option will not appear if preferences have been imported from an earlier release of Discovery Studio. Use the Reset button on the

Edit > Preferences > Files Explorer > URL Location page to load the new site.

DSC-33797

A script to color AlphaFold proteins by their per-residue confidence score was added to the Scripts > Visualization menu.

DSC-33798

A new prototype component “Calculate Sequence Descriptors” was added to the Sequence Analysis collection. The component calculates protein molecular and residue descriptors from input sequences. If the input is an antibody, antibody domain and CDR descriptors can be calculated.

DSC-29794

Reduced the ring and bond distortions in the Show 2D Diagram in the Discovery Studio Client when visualizing Receptor Ligand Interactions. For complex ring systems, slight distortions could still be visible, but they do not affect the interaction perception.

DSC-33102

Protocols using CHARMm now run correctly on Linux when user names contain white spaces.

DSC-33134

Fixed an issue in the Calculate Protein Ionization component so that the molecular net charge will be reported when the At pH parameter is set to 10.

DSC-33239

Fixed an issue with the Discovery Studio Client where the Protocol Explorer would not load correctly when the Change Server dialog was used to reconnect to the same server and https or the port number were omitted.

DSC-33270

Fixed an issue in the Generate Analog Conformation protocol to avoid failures when input ligands contain the DontMapAtoms property.

DSC-33315

Updated the Antibody Modeling Cascade protocol to ensure that the final model will be a CDR-refined model if the Loops to Model parameter is defined, even if the framework model before CDR loop refinement has lower PDF total energy.

DSC-33434

Added a warning to the Type Ligands with MATCH (Prototype) protocol for instances when the input ligand may have an incorrect number of hydrogens or incorrect formal charges.

DSC-33439

The Assign Forcefield protocol now correctly assigns customized nucleotide templates.

DSC-33441

Fixed a Discovery Studio Client issue where the Jobs Explorer could show a “Session ID invalid” message for a running job when connecting to the same server.

DSC-33442

Fixed an issue where the Discovery Studio Client’s context menus did not display correctly on a secondary monitor on Windows operating systems.

DSC-33459

Fixed an issue that was causing the Update Antibody Database example protocol to fail when the Destination Directory parameter was specified as a folder under the userdata shortcut.

DSC-33500

The Generate Novel Ligands protocol no longer fails when a ligand contains multiple fragments, or ions.

DSC-33514

Improved error handling of invalid SMILES in the Replace Fragment protocol. Also corrected invalid SMILES entries in the Replace Fragment default databases.

DSC-33545

Reduced the memory usage of solvated systems when running Simulation protocols such as Calculate Energy.

DSC-33750

Open URL with the Default Sequences Site and the DS API CreateFromSequenceId stopped working with some forms of ID due to a change at NCBI. The examples in the documentation have been updated to include valid IDs.

DSC-33783

Fixed the help link for the CHARMm Relative FEP Calculations (GPU) and MSLD Bias Optimization and Production protocols.

DSC-33786

Fixed a Discovery Studio Client issue where the help page did not open for some Tool Panel links.

DSC-33829

The legends in the Discovery Studio Client 3D views are now scaled dynamically.

DSC-33899

The RCSB search API terms needed for the Chemical Component, Full Text, and Exact ligand query changed in 2021. The RCSB Structure Search protocol has been fixed to generate the new terms.

DSC-33926

Fixed an issue where the clustering dendrogram created from the All Frames RMSD calculation in the Analyze Trajectory protocol only linked to the first 999 conformations of the associated trajectory.

DSC-33960

Fixed an issue where the Discovery Studio Linux Client did not recognize symbolic links to directories in the Files Explorer.

DSC-33983

Removed the Pipeline Pilot SERVER connection option for the Windows client wide-scale deployment due to server authentication requirements.

DSC-33984

Resolved an issue that was causing the Windows Discovery Studio Client to become unresponsive on some machines when files were opened by double clicking.

DSC-28286

The Generate Analog Conformations protocol will now return an error if there is no analog conformation generated (for example, due to invalid input lead or analog ligands).

DSC-33094

Renamed several fields in the Preferences > General > Script Command page in the Discovery Studio Client Preferences to be more indicative of their function (Tooltip title and Tooltip text).

DSC-33135

The Discovery Studio Client Protocols Explorer now only lists the current user’s folder (in addition to the standard Discovery Studio and Example folders).

DSC-33497

Enhanced the Type Ligands with MATCH (Prototype) protocol to better handle typing failures.

DSC-33580

The Update BLAST Databases protocol will now correctly expand shortcuts in file and directory names. In addition, the verification of the generated databases has been enhanced by running a test search.

DSC-33718

Fixed a Dock Proteins (ZDOCK) protocol issue where jobs were failing because of a missing libmkl_avx512.so library on machines with newer Intel® AVX-512 chips.

PPP-46872

Fixed an issue where certain /xinfo/ based REST services would fail with 500 Http error codes if the Pipeline Pilot server was configured with a Remote Protocol Database ("XMLDB Endpoint" setting in the Pipeline Pilot Administration Portal). This caused failures when the Pipeline Pilot server was configured in this fashion with 2021 Pipeline Pilot client applications reliant upon those REST services such as Discovery Studio, Materials Studio, and Insight.