Program
BIOVIA Discovery Studio
Operating System
All supported operating systems
Description
We are providing this Technical Note to inform you about the release of BIOVIA Discovery Studio 2025 which includes the following enhancements and fixed defects:
Enhancements
This release of BIOVIA Discovery Studio includes the following enhancements.
| User Story | Description |
|---|---|
| DSC-35676 | Discovery Studio for Windows is compiled using Visual Studio 2019. |
| DSC-36103 | The antibody templates database is now installed using two packages. |
| DSC-36958 | The method for setting the Germline Source parameters in the Annotate Antibody Sequences protocol is simplified, which improves performance. |
| DSC-37191 | The help text for Use Secondary Structure parameter in the Align Sequences protocol is improved. |
| DSC-37472 | The example report images in the Toxicity Prediction (Extensible) help text are updated. |
| DSC-37488 | The Discovery Studio server now uses the Materials Studio package for QM-MM calculations. |
| DSC-37551 | The Discovery Studio system requirements now include the required Linux libraries for the License Pack software. |
| DSC-37584 | The PharmaDB Profiler protocol now stores the function information in a CSV file, and includes the total entries that map for the function as an additional property. |
| DSC-37591 | PharmaDB is updated based on scPDB release 2024 (http://bioinfo-pharma.u-strasbg.fr/scPDB), and now contains over 41,000 entries. The database was built using the Diverse option for Pharmacophore Scoring Method. |
| DSC-37692 | Detailed information for updating licenses is now available in the Discovery Studio help under Managing Discovery Studio > Licensing > Licenses |
| DSC-37705 | You can now set the DiscoveryScript API PDBName property. |
| DSC-37737 | The Solvate with Explicit Membrane protocol is updated to include improved constraints during equilibration, which results in better equilibrated and solvated systems. |
| DSC-37755 | The PDB Ligand Bond Orders script is upgraded to use Chemical Component Dictionary files to assign bond orders and formal charges to all ligands and other small molecules read from RCSB PDB files. |
| DSC-37872 | The Dock Proteins (ZDOCK) protocol no longer has a chain name length restriction for the input proteins. |
| DSC-37916 | MPI is updated to version 2021.11. |
| DSC-37959 | Documentation is now available for the mmCIF file format, and biological assemblies read in mmCIF format are now correctly named. |
| DSC-37962 | When you attempt to import a CIF file that contains reflection data rather than molecular data, the error is now flagged with an appropriate message. |
| DSC-37996 | Information about residues in the sequence of a macromolecule that is missing from its structure is now read from mmCIF files. This allows the missing residues to be shown in the Protein Report and modeled using Build and Edit Proteins tools. |
| DSC-38011 | The GPU version of Dock Proteins (ZDOCK) now uses CUDA 11.4. |
| DSC-38127 | Perl is updated to version 5.36.3. |
| DSC-38128 | The xerces library is updated to version 3.2.5. |
| DSC-38130 | The zlib library is updated to version 1.3.1. |
| DSC-38149 | CCDC GOLD version 2024.1 is now supported. The torsions sampled by GOLD during docking are improved. A new Flexibility parameter, Torsion Angle Distribution, is available in the Dock Ligands (GOLD) protocol. |
| DSC-38208 | The following packages are no longer required when installing the Discovery Studio server: clientsdk, dataaccess, waf, hub, and binstore. |
| DSC-38243 | A new internal component, Write mmCIF Files (Prototype), saves data records in mmCIF format. |
| DSC-38254 | The RCSB Structure Search protocol now reads mmCIF format files by default, which allows all hits to be read. |
| DSC-38372 | A new package, bioviapytorch, is added to support antibody paratope prediction. |
| DSC-38461 | The Prepare Germline Sources protocol now uses the ClustalW2 engine to align sequences. |
| DSC-37312 | Discovery Studio requires an installation of Pipeline Pilot 2025. |
| DSC-37713 | Secondary structure definitions can now be read from mmCIF files into the PDB Secondary property, and displayed in the same way as those read from PDB files. |
| DSC-37883 | MODELER is updated to version 10.5 and compiled with python 3.12. |
| DSC-38091 | Chemical component definition (CCD) records are now read from mmCIF structure files, enabling ligand bond orders and formal charges to be assigned correctly. |
| DSC-38411 | OpenSSL is updated to version 3.0.15. |
| DSC-38436 | A new component, Antibody Paratopes Prediction, predicts the antigen binding site residues in antibody CDR loops. |
| DSC-38438 | A new protocol, Predict Antibody Paratopes, predicts the antigen binding site residues in antibody CDR loops. |
| DSC-38174 | SQLite is updated to version 3.45.3. |
| DSC-36371 | Discovery Studio for Linux is compiled on the Red Hat 8 platform using a GCC 8 compiler. |
| DSC-36925 | The Interaction Pharmacophore Generation protocol now supports producing a diverse set of pharmacophores in addition to top scoring pharmacophores. |
| DSC-37590 | The Dynamics (NAMD) protocol has a new parameter, Enable GPU-Resident Mode, which handles GPUs better for improved performance on Linux. |
| DSC-37709 | Discovery Studio MOL2 format files can now store multicharacter chain names. |
| DSC-38085 | Discovery Studio is compiled with strict conformance to the C++ 17 standard. |
| DSC-37701 | The PDB Name attribute character limit is increased from three to five characters. |
| DSC-38413 | Qt is updated to version 5.15.17. |
Fixed Defects
This release of BIOVIA Discovery Studio includes the following fixed defects.
| User Story | Description |
|---|---|
| DSC-37615 | Dynamics (Production), Dynamics (NAMD), GaMD Equilibration, and GaMD Production protocols were fixed to allow the Simulation Time parameter to specify values greater than 200 ns. |
| DSC-37760 | The Create Pharmacophore Manually tool panel now handles the new pharmacophore feature types (e.g., iHBA, iHalogen, etc.) correctly. |
| DSC-37987 | A problem with retrieving templates added by the Update Antibody Database protocol has been corrected. |
| DSC-38400 | The Calculate Mutation Energy (Stability) and Calculate Mutation Energy (Binding) protocols are updated to reduce differences in energy values when running on different operating systems. Also, the Discovery Studio Help has been updated to provide better guidance on the application of the results. |
| DSC-38516 | Files are no longer incomplete if there are network instabilities during download from the Pipeline Pilot server. |
| DSC-34377 | Changing fonts and zooming in and out of a 2D Diagram no longer causes the client to stop working. |
| DSC-36320 | BLAST databases created with the makeblastdb.exe executable can now be moved to another location for use. |
| DSC-37212 | Prepare Protein protocol no longer fail for inputs having more than 99999 atoms, including hydrogen atoms added by the protocol. |
| DSC-37252 | The Example protocol Recenter Solvated System Trajectory provides proper messaging when the input DSV contains no conformations. |
| DSC-37288 | The HT-XPIPE protocol now runs successfully. |
| DSC-37403 | The Linux system library compat-libstdc++-33 is no longer required and has been removed from the System Requirements document. |
| DSC-37539 | Analyze Trajectory now returns non-bond interaction data when the input trajectory contains more than 10,000 frames. |
| DSC-37542 | The Analyze Trajectory protocol now returns bond/torsion monitoring data. |
| DSC-37556 | An issue where the Calculate Aggregation Scores protocol may have returned the wrong trajectory frames when you changed the Frame Start and Frame End default values is fixed. |
| DSC-37662 | Fixed an issue where the Discovery Studio client created a memory dump upon exit under certain conditions. |
| DSC-37721 | The Estimate Free Energy Landscape protocol now runs when only an input CSV file is provided for the Input Data parameter. |
| DSC-37892 | The Generate Conformations protocol now correctly uses the selected setting of the Implicit Solvent Model parameter. |
| DSC-37920 | The Create Pharmacophore Manually tool panel no longer allows users to create incompatible Point features (e.g., Ring_Aromatic_Centroid). |
| DSC-38124 | The Recenter Solvated System Trajectory example protocol no longer fails when creating a group from selection as input. |
| DSC-38126 | Inserting a structure from mmCIF format will no longer create spurious intermolecular bonds. |
| DSC-38632 | Added a timeout to avoid long 2D depiction rendering times for some large flexible ligands. |
| DSC-38799 | Extended CHARMm's ability to handle extra-large molecular systems (up to 1 million atoms). |
| DSC-31206 | The Update Antibody Database example protocol now removes all terminal residues which are not standard amino acids. This prevents invalid templates from being created. |
| DSC-38454 | Importing mmCIF files with multiple models which cannot be processed as conformations will now create a set of molecules containing the appropriate atoms. Previously all atoms were placed in the first molecule. |
Resolution
BIOVIA Discovery Studio 2025 was released in November 2024 and is available for download at https://software.3ds.com under BIOVIA products and can be found under:
Product line: Lab, Scientific and Content Solutions
Release: BIOVIA 2025
Level: BIOVIA 2025 Golden
Fixes for this level: -
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If you have any questions, please contact BIOVIA Support.
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