DSC-34046

The parameters for the Example utility protocols Download BLAST DB Files and Update BLAST Databases are simplified and the help text is clarified.

DSC-34223

Discovery Studio Client now displays the Run On Grid parameter group only when the server is connected to a Pipeline Pilot Server that is configured on a grid.

DSC-34366

A utility protocol, Build PDB Reference Data, which processes PDB ligand information for use with the RCSB Structure Search protocol, is moved to Examples.

DSC-35533

All occurrences of ftp://ftp.wwpdb.org are updated to https://files.wwpdb.org in Discovery Studio Client and all relevant protocols

DSC-35660

The PDB, PDB_nr95, and Swiss-Prot BLAST databases are updated using data available as of May, 2023.

DSC-35661

The third-party clustering data used for generating the PDB_nr95 BLAST database is now defined by entity rather than by chain. The Download BLASTDB protocol now downloads the new file, and the Update BLAST Databases protocol now processes this data to map it to the chains in PDB files. Also, the URLS used to download the third-party data used to generate the databases are changed to https.

DSC-35664

The Operating System information in the charmm.log files is now truncated to not reveal specific OS details. For example, "Microsoft Windows [Version 10.0.14393]" is now truncated to "Windows."

DSC-35682

The Enumerate Ligands for MSLD protocol no longer fails when custom substituents have trailing spaces.

DSC-35721

Discovery Studio 2023 SP1 is compatible with Pipeline Pilot 2023 SP1 server.

DSC-35731

Qt Windows libraries are upgraded to version 5.15.10 to address security vulnerabilities.

DSC-35744

The PharmaDB is updated based on the scPDB release 2022 (http://bioinfo-pharma.u-strasbg.fr/scPDB), and now contains over 37,000 entries.

DSC-35765

The Antibody Database is updated with 6711 antibody structures from the PDB database release of July 2022.

DSC-35766

The Update Antibody Database example protocol now supports lower-case chain names in PDB files.

DSC-35770

The Filter by SMARTS protocol has a new option to filter ligands by PAINS (Pan Assay Interference Compounds) substructures.

DSC-35772

The Ligand Profile (Deprecated) component, with GUID: {859441F0-6D93-CE43-0452-F7697170DCF0}, is no longer available. Remove this component from your custom protocols.

DSC-35773

The Ligand Profiler protocol now adds shape similarity properties (4FeatShape#ShapeSimilarity and 4FeatShape#PercentFilled) to the output ligands.

DSC-35791

The Predict Humanizing Mutations protocol now shows flyover tooltip residue details in the report.

DSC-35812

The Prepare Germline Sources example protocol has improved error handling and reporting.

DSC-35871

The performance of the Dock Ligands (GOLD) protocol is improved.

DSC-35902

Dock Ligands (GOLD) supports CCDC GOLD 2023.

DSC-35931

The Predict Excipient Interactions protocol is now compatible with the Python version included with the current version of Pipeline Pilot.

DSC-35936

Discovery Studio now requires an installation of Pipeline Pilot 2023 SP1.

DSC-36040

The maximum system size for Dock Proteins (ZDOCK) was increased from 169 Å to about 200 Å (depending on the settings).

DSC-36083

The performance of the Dock Proteins (ZDOCK) protocol is improved by 10-20%, depending on the settings.

DSC-36087

Help for sequence motifs and domain filtering in the Predict Sequence Properties protocol has been clarified.

DSC-36204

The conformation that represents the cluster center is now shown when selecting a node in the dendrogram generated by the Analyze Trajectory protocol.

DSC-36209

The residue database for the RCSB Structure Search protocol is updated based on the PDB release from May 2023, which contains 40,322 residue entries.

DSC-36436

The error message for attempting to connect the Discovery Studio Client to a Pipeline Pilot Server that does not have the Discovery Studio Collection installed is improved for usability.

DSC-36521

Two new protocols, PharmaDB Filter and PharmaDB Profiler, to filter the PharmaDB using various properties and to map a set of ligands against the filtered pharmacophores, are available from the Pharmacophore Search, Screen, and Profile tool panel. The Input Pharmacophore Database options have been removed from the Ligand Profiler protocol.

DSC-35757

A new protocol, GaMD Production, allows you to run and restart Gaussian accelerated Molecular Dynamics simulations.

DSC-35758

A new protocol, GaMD Equilibration, is added that allows the user to configure a Gaussian accelerated Molecular Dynamics simulation and automatically parametrize boost potentials.

DSC-35760

CHARMm is upgraded to version 47b1.

DSC-35761

The MSLD Bias Optimization and Production protocol is updated to use the BLaDE software, which results in a significant speed increase.

DSC-35775

The Assign Forcefield and Type Ligands with MATCH (Prototype) protocols expand chemical space coverage with an option for assigning charges through an ML model trained on ESP-fit QM data, and torsion parameters that are generated by fitting to QM data.

DSC-35797

The Protein Formulation Property Calculator component, used by the Calculate Protein Formulation Properties protocol is improved for efficiency.

DSC-35798

A new tool panel, Run Enhanced Sampling Simulations, provides access to the GaMD Production and GaMD Equilibration protocols. The existing Analyze Trajectory tool panel now includes the Measure Trajectory Features, Estimate Free Energy Landscape, and Cluster Conformations protocols.

DSC-35799

The performance of the Assign Forcefield protocol is improved for charmm36.

DSC-35942

The error handling in the DS Protein Sequence Reader and DS Nucleotide Sequence Reader components is improved.

DSC-36022

The following enhancements were made to the Predict Humanizing Mutations protocol. A published machine learning (ML) method was added that uses a large-scale antibody sequence database to build classifiers that can distinguish between human and murine sequences. The residue frequency data was updated using a large new data set. Identity/similarity to the query sequence for the various substituted sequences has been added along with their 'humanness' scores. The residue reports now show the positions of the interface residues, and the positions of the Vernier residues are highlighted. Chain breaks have been added to the sequences in the Residue Substitutions alignment to match the Query sequence.

DSC-36031

A new protocol, Estimate Free Energy Landscape, estimates a free energy landscape from a data set or a set of simulations, allowing for statistical reweighting of GaMD simulations. A new protocol, Measure Trajectory Features, measures time-series features (such as SASA, RMSD, Dihedrals) from molecular dynamics trajectories for further analysis. A new protocol, Cluster Conformations, discretizes conformational states from simulation trajectories.

DSC-36068

The antibody template data has been reorganized.

DSC-36216

The trajectory animations in the Discover Studio client now include frame numbers. Additionally, you can change the current frame by moving a slider.

DSC-36442

Custom BLAST and antibody databases are now stored and utilized from the <pp_install>/public/DS directory.

DSC-35900

Several protein modeling protocols, Prepare Protein, Calculate Protein Ionization and Residue pK, Calculate Mutation Energy (Binding), Calculate Mutation Energy (Stability), and Calculate Protein Formulation Properties now support the charmm36 forcefield.

DSC-35929

Discovery Studio Client can now be installed on Windows 11.

DSC-35944

The script for displaying germline sequences in Annotate Antibody Sequence contained a server file path, which could be incorrect but was unnecessary, so has been removed.

DSC-34075

The Calculate Mutation Energy (Stability) and Calculate Mutation Energy (Binding) protocols no longer fail when input is typed with the charmm36 forcefield and when the protein has neutral N- and C-termini or deprotonated CYS and TYR residues.

DSC-34611

A crash which could occur in the Calculate Aggregation Scores, Calculate Protein Formulation Properties and Predict Excipient Interactions protocols if using the Chinese version of Windows has been fixed.

DSC-35494

The 2D binding site diagram now displays steric bumps.

DSC-35649

The upgrade to a newer version of MPI libraries resolves MPI issues on certain hardware such as dual-socket motherboards for Simulation protocols.

DSC-35674

Added angle PO4-OT-HO parameter for CHARMm forcefield so that molecular system with HPO4 (-2) and H2PO4 (-1) anions runs simulation successfully.

DSC-35751

Corrected the "5 rotatable bonds" option of the Filter by SMARTS protocol.

DSC-35806

Fixed an issue in the DiscoveryScript CreateCell API that was causing client instability when length values of 0 were passed.

DSC-35807

The Discovery Studio Simulation PDB exporter used to store the "Segment ID" atom property even if its length exceeded the column width allowed by the PDB file format specification, resulting in file corruption. Now the PDB exporter only writes the first four significant characters of a "Segment ID" atom property.

DSC-35808

Fixed an issue where an ARG side-chain deprotonated using the Modify Protonation State feature was typed as unknown using the CHARMm Polar H forcefield.

DSC-35818

The naming of oxygen atoms at protein C-termini has been updated to ensure correct typing with the charmm36 forcefield.

DSC-35943

Input Sequence Alignment is now a required parameter for the Align Sequence Profiles protocol.

DSC-35975

The Align Structures protocol no longer fails to generate the final results property when the first cluster consists of a single protein.

DSC-35987

The Microsoft MSVCP140_1.dll redistributable is now included in the Windows Discovery Studio client installer.

DSC-36008

Fixed an issue where the example protocol Download BLAST DB Files failed.

DSC-36038

Addressed an issue of the Dock Ligands (CDOCKER) protocol, where 2D input ligand structures may be docked outside the binding site sphere.

DSC-34734

Fixed an issue where the Discovery Studio client may reset protocol parameters to the default values when changing or reconnecting to a server.

DSC-35588

The Predict Humanizing Mutations protocol was corrected to perform energy calculations if the suggested substitutions are all within one chain

DSC-35809

The Discovery Studio Simulation PDB importer now assigns each section of a PDB file terminated by an END record to a separate molecule. If the molecules have matching residues and atoms, only one molecule is kept and the remaining molecules are converted to conformations.

DSC-35978

Corrected the total charge of deprotonated tyrosine patch, PRES TYRD, in charmm36 forcefield to avoid warnings in the charmm.log file.

DSC-36151

The Build Homology Models, Model Antibody Framework and Add Membrane and Orient Molecule protocols now have appropriate final messages if there is an error.

DSC-36228

Added the missing link to the help text on the Antibody Modeling Cascade protocol dialog Help button.

DSC-36339

An empty database will no longer persist if the Database 3D Build protocol fails to build a database.

DSC-36352

Server error messages are now always written using ASCII.

DSC-36470

The handling of unexpected errors while building antibody models in the Antibody Modeling Cascade and Predict Humanizing Mutations protocols has been improved.

DSC-36520

The hits returned by the RCSB Structure Search protocol are now filtered according to whether they are pdb format-compatible.