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Jan 28 2021

T10-2021 Notification regarding BIOVIA Discovery Studio 2021

BIOVIA Discovery Studio

BIOVIA Discovery Studio

Operating System

Server Operating Systems:

Microsoft Windows Server 2016 and 2019 (64 bit)

Microsoft Windows 10 (64 bit) standalone or single-user

CentOS 7.5+ and 8.1+ (64-bit)

Red Hat Enterprise Linux 7.5+ and 8.1+ (64-bit)

Client Operating Systems:

Microsoft Windows 10 (64 bit)

Red Hat Enterprise Linux 7.5+ and 8.1+ (64-bit)

Description

We are providing this Technical Note to inform you about the release of BIOVIA Discovery Studio 2021 Golden that includes the following enhancements and fixed defects:

Enhancements

This release of BIOVIA Discovery Studio includes the following enhancements.

DSC-17616– The steps to migrate Catalyst databases to a new installation have been expanded in the server installation documentation.

DSC-30841– Improved the pseudo chirality perception in the Common Feature Pharmacophore Generator and Pharmacophore Ensemble Generation protocols, where in rare cases the conformational models were incomplete.

DSC-32397– Replaced the obsolete GFF Feature Writer in the DS Alignment Writer component with the GFF Writer component.

DSC-32530– Improved the file download speed for the Predict Humanizing Mutations protocol by zipping the output files.

DSC-32031– Added a new Advanced parameter 'Keep Initial Orientation' to Calculate Electrostatics Potential to preserve the input molecule orientation.

DSC-24124– The Ligand Profiler protocol now reports the selectivity score and types of features for PharmaDB pharmacophores that map the input ligands.

DSC-30821, DSC-31433– CHARMm is upgraded to support CUDA 10.1 for GPU computing for the following protocols: Dynamics (Production), MSLD Bias Optimization and Production, and CHARMm Relative FEP Calculations (GPU).

DSC-31276– Production (Dynamics) protocol run with OpenMM platform automatically recenters solvated systems.

DSC-31358, DSC-31468– An option to use GPU acceleration was added to the Dynamics (NAMD) protocol.

DSC-31427– The following deprecated protocols and components were removed from the release:
Align Multiple Sequences (Deprecated), Predict Stabilizing Mutations (Deprecated), Build Models (Deprecated), Mutation Energy (Binding) (Deprecated), Mutation Energy (Stability) (Deprecated), Protein Preparation (Deprecated), Find Antibody Domains (Deprecated), CHARMm Binding Energy (Deprecated), CHARMm In Situ Ligand Minimization (Deprecated), CHARMm Minimization (Deprecated), Convert Hits to Alignments (Deprecated), Create BLAST Profile (Deprecated), Analyze Ligand Poses (Deprecated), Pose Analysis (Deprecated), 3D Database Search (Deprecated), Database Build 3D (Deprecated), Shape Search (Deprecated), Discovery Studio Viewer (Deprecated), Delete Files (Deprecated), Remove Directory (Deprecated), Write Plotting Script (Deprecated), MSV Small Molecule Reader (Deprecated), Selected Core Reader (Deprecated), Small Molecule Selected Core Reader (Deprecated), Modify Report Links (Deprecated).

DSC-31442– Discovery Studio 2021 is built on Pipeline Pilot 2021.
PERL is updated to version 5.30.

DSC-31458– The FEP workflow now supports transformations involving chirality differences not included in a ring.

DSC-31536– Complex system prepared using the Set Up MSLD Calculations protocol can now be optionally used as input for the Collate MSLD Simulation Results protocol.

DSC-31539, DSC-31970, DSC-32604– Added an option to the Dock Proteins (ZDOCK) protocol to use GPU acceleration, and improved the performance when running on CPU.

DSC-31551– The PharmaDB pharmacophores available from the Ligand Profiler protocol have been regenerated using non-bond interactions.

DSC-31562– Added an option to the Solvate with Explicit Membrane protocol to use GPU acceleration when equilibration is selected.

DSC-31623– Discovery Studio Server now supports RedHat 8 and CentOS 8.

DSC-31662– Discovery Studio Client and server now support the latest available OpenSSL 1.1.1 version.

DSC-31757, DSC-32675–The Calculate Protein Formulation Properties protocol now displays surfaces colored by the surface charge map and aggregation scores. The surfaces are added to structures, which are opened via links in the report table.

DSC-31800– Updated the Pipeline Pilot perception of Nitrogen hybridization atoms to be in better agreement with generally accepted rules (for more information, see the Pipeline Pilot release notes).

The changes may affect the results of the following protocols:

  • ADMET Descriptors
  • Toxicity Prediction (Extensible)
  • Calculate Molecular Properties
  • Calculate Ligand Efficiency
  • Filter by Lipinski and Veber Rules
  • Prepare Ligands
  • Find Similar Molecules by Numeric Properties
  • Ensemble Pharmacophore Generation
  • Enumerate from Fragments
  • Create Bayesian Model
  • Create Genetic Function Approximation Model
  • Create Multiple Linear Regression Model
  • Create Partial Least Squares Model
  • Create Recursive Partitioning Model
  • Prepare Ligands for QSAR
  • Generate RECAP Fragments
  • Grow Scaffold
  • Replace Fragment

DSC-31803– Added new functionality to the Calculate Molecular Properties protocol that allows learner xml files to be specified.

DSC-31812, DSC-31716– Template force field files used in the Type Ligands with MATCH protocol were updated to CGenFF 4.1.

DSC-31822– Removed a note from the help for the Input Ligands parameter that referred to performance enhancement when copying to a local server.

DSC-31823– The CHARMm version in Discovery Studio is updated to 44b2.

DSC-31825, DSC-31927– Added an Optimize Bond and Angle Parameters component to optimize small molecule force-field parameters pertaining to bond and angle terms.

DSC-31833– The units of concentration for Ki (mol/L) in the Ligscore1 and Ligscore2 scores was added to the Receptor-Ligand Interactions documentation.

DSC-31835– Improved the documentation for creating a customized pharmacophore feature using SMARTS.

DSC-31890, DSC-32297–Non-bond pharmacophore features are now available in the ligand-based pharmacophore protocols, including 3D QSAR Pharmacophore Generation, Common Feature Pharmacophore Generation, Ensemble Pharmacophore Generation, and Features Mapping. The new features are available as an option in the Features parameter, and are accessible from the Edit and Cluster Features tool panel.

DSC-31893– Implemented a new hierarchical atom typer in MATCH and made necessary modifications to the underlying relation matrices to utilize updated CGenFF parameters.

DSC-31914, DSC-32001– Added a new protocol, CHARMm FEP Calculations (GPU), to run FEP calculations using the DOMDEC GPU platform.

DSC-31949– Added parameters to the Annotate Antibody Sequence and Predict Humanizing Mutations protocols to load germline data files from any location. It is no longer required to copy the files into the installation folder.

DSC-31950– Data used by protein modeling protocols are now stored in the <pps_install>/apps/scitegic/dsdata and <pp_install>/apps/scitegic/dsblastdata directories. Some user data, such as BLAST databases can still be added under the <pps_install>/public/DS directory.

Note: When upgrading a Pipeline Pilot server installation you may see Antibody data in <pps_install>/public/DS/Antibody directory, which is no longer required and can be deleted.

DSC-31981– Adjusted the polling interval, timeout value and Batch Search parameters used within the BLAST Search (NCBI Server) protocol to match NCBI recommendations. This should provide more stable access to the NCBI servers when performing a sequence similarity search. The accession number in BLAST databases was changed to no longer include database names, so the protocol has been altered accordingly.

Inconsistencies have sometimes been observed between the hits found and the sequences retrieved from the NCBI databases. The error handling in the protocol now allows the job to complete with a warning rather than error.

DSC-31992– Added a new parameter, Custom Parameter File, to the Type Ligands with MATCH (Prototype) protocol to support custom parameter files.

DSC-32004– The Set Up MSLD Calculations protocol now supports Orthorhombic crystal shape, allowing smaller solvated systems.

DSC-32005, DSC-32388, DSC-32534– Data files from the dscore package were migrated to a new dsdata package. The GrowScaffold folder in the public directory is now located in the dsdata package.

DSC-32015– Removed the "Add Folder..." option from the Protocols Explorer context menu.

DSC-32028– Example protocols are now always exposed in the Discovery Studio Client Protocols Explorer.

DSC-32082– Added a new script to the Discovery Studio Client Samples | Scripts folder to copy the protein display color from a reference protein into other proteins in the same active Molecule Window.

DSC-32083– RCSB announced that legacy search APIs will be discontinued from November 2020. Therefore, the RCSB Structure Search protocol has been updated to use their new APIs. The same or equivalent searches are supported, wherever possible. The Motif search now allows searching using Prosite-type motifs or regular expressions, and can be applied to protein, DNA or RNA sequences. However, sequence similarity searches and downloading JSON queries from RCSB are not available from RCSB. Additionally, the HasLigand filter is no longer supported.

DSC-32094– The Discovery Studio Client is now compatible with Red Hat 8.

DSC-32192– Added an internal component to the MSLD Bias Optimization and Production protocol to run MSLD production simulations in parallel.

DSC-32193– Discovery Studio 2021 is now compatible with the CCDC GOLD 2020.

DSC-32200, DSC-32396, DSC-32282– The template structures in the Antibody Database are now stored in a compact binary format rather than as .mol2 format files. This reduces the amount of disk space required. As a result, all templates, including the redundant templates are part of the Discovery Studio server installation. An example protocol Retrieve Antibody Templates from Database is provided to allow specific templates to be retrieved and saved as mol2 files. The Update Antibody Database example protocol is updated to handle this compact file format.

DSC-32218, DSC-32507– The location of the BLAST databases used for local BLAST and PSI-BLAST searches has been changed to <pps_install>/apps/scitegic/dsblastdata. The PDB and Swiss-Prot databases we generate are now included in the standard installation along with PDB_nr95 and antibody_variable.

DSC-32232, DSC-31520, DSC-32049, DSC-32670, DSC-32717, DSC-31272– Added a new protocol, MSLD Bias Optimization and Production, to combine bias optimization and production functions in MSLD calculations. This protocol replaces the MSLD Bias Optimization and MSLD Production protocols, which are deprecated and removed from the tool panel.

DSC-32256– Updated the ligand database for the RCSB Structure Search protocol based on the PDB release in July 2020 with 32,522 ligand entries.

DSC-32257– Updated the BLAST databases. PDB_nr95 and PDB now include sequences from the July 2020 PDB release. Swiss-Prot is updated to the latest version from UniProt.

DSC-32258– Updated the Antibody database according to RCSB PDB as of July 2020.

DSC-32295– Upgraded to MODELER 9.24.

DSC-32296– The BIOVIA Catalyst databases are moved from <pps_install>\public\DS\CatalystDB to the <pps_install>\apps\scitegic\dsdata\data\CatalystDBs folder.

DSC-32300– The MSLD Bias Optimization and Production protocol now restrains the center of mass of ligand in free ligand simulation systems, preventing drift.

DSC-32303, DSC-25681, DSC-27170– Upgraded Qt to version 5.12 on Windows to support 4K monitors.

DSC-32304– The Discovery Studio Client now uses the Chromium-based web page rendering on Windows.

Note that on Windows, the HTML viewer does not support the View page source and Save page commands.

DSC-32312– The full PharmaDB database is now available from the Ligand Profiler protocol after a default installation.

The new PharmaDB database is located in <pps_install>/apps/scitegic/dsdata/data/PharmaDB.

Note: When upgrading a Pipeline Pilot server installation you may see PharmaDB data directories (PharmaDBv3 or PharmaDB) in <pps_install>/public/DS/. These directories are no longer required and can be deleted.

DSC-32320– Added two options to the Use Composition Based Statistics parameter in the BLAST Search (NCBI Server) protocol, and adjusted its default setting and the default for the E-value Cutoff to align with current NCBI recommendations.

DSC-32440– Added optimized bond and angle parameters to the Charmm36 small molecule force field.

DSC-32447– Removed the dependency on the Pipeline Pilot GPL Installer for Biology Collections for all of the Discovery Studio protocols on Linux, except for the Predict Sequence Properties protocol.

DSC-32482– The Set Up MSLD Calculations protocol now limits the number of bonds per atom in the multi-topology molecule, and removes atoms from the common core to meet this constraint.

DSC-32575– Enhanced the Collate MSLD Simulation Results protocol to combine data from multiple trajectories.

DSC-32576– Updated the Grid Options parameter in the Dynamics (Production), Dynamics (NAMD), and Solvate with Explicit Membrane protocols to include Number of GPUs.

DSC-32589– Atoms in the multi-topology ligand created by Set Up MSLD Calculations protocol now have shorter names based on sequential numbering for each input ligand.

DSC-32695– MSLD systems prepared in the Set Up MSLD Calculations protocol are now output to a single mol2 file.

DSC-33064– Updated OpenMM to 7.4.2 for use in the OpenMM GPU platform in Dynamics (Production) protocol.

This release of BIOVIA License Pack includes the following enhancements.

LPK-559– The License Pack now uses FlexLM 11.16. The License Pack on the license server must be the highest version installed on the network. Ensure that you update the License Pack on the license server to this version to enable the checkout of licenses on client machines.

Fixed Defects

This release of BIOVIA Discovery Studio includes the following fixed defects.

DSC-32633– Improved the stability of the Clean Protein functionality.

DSC-31943, DSC-31931– Fixed an issue with the Discovery Studio Client where the File | Open URL command did not open secure html pages for some servers.

DSC-32531– Addressed a Discovery Studio Client instability caused by the DiscoveryScript::Documents scripting method.

DSC-27405– The plot generated in the Optimize Subset Library with Pareto Method protocol now opens the represented sd files when selected.

DSC-28758– Reduced the cryptic messages when launching the Discovery Studio Client on Linux from the command line.

DSC-31039– The GTGN (neutral form of guanine-triphosphate-gamma-sulphur residue) can now be typed by the Assign Forcefield protocol.

DSC-31212– Removed some duplicate residues and corrected some residues with long names in the charmm36 forcefield so that they can be typed properly.

DSC-31325, DSC-31684– Removed options to change the installation location of the Linux License Pack.
The Linux version of the Discovery Studio Client installer now installs the License Pack parallel to the client.

DSC-31344– Fixed an issue where the View Results script from the Align Structures protocol produced an error when some structures were not aligned.

DSC-31411– The Charts Display Style Dialog now works as expected when changing Fonts, using Set As Default, and clicking OK.

DSC-31513– The Attributes dialog is now shown for 3D objects selected in both the molecule window and a 2D diagram.

DSC-31584– Fixed an error in the Solvate with Explicit Membrane protocol so that the starting time in the charts in the report is always 0.

DSC-31603– Fixed an issue with protein ionization calculations where the protonation state was not predicted correctly when the molecular system had atomic coordinates smaller than -99.999 or larger than 999.999. This fix affects the following protocols:

  • Calculate Mutation Energy (Binding)
  • Calculate Mutation Energy (Stability)
  • Calculate Protein Formulation Properties
  • Calculate Protein Ionization and Residue pK
  • Prepare Proteins

DSC-31622, DSC-32332– The Predict Humanizing Mutations protocol no longer reports an error when no mutations are found, and reports the information instead.

DSC-31687– The Prepare Germline Sources protocol can now correctly process sequences that contain pipe characters in their names.

DSC-31731– The Molecules to Conformations script in the Scripts menu now runs correctly if the input molecules have locked visibility.

DSC-31759– Fixed an issue with the 2D structure depiction of triple bonds in the Discovery Studio Client.

DSC-31779– The Generate Analog Conformations protocol now correctly reports an error message when no conformations are generated.

DSC-31826– Fixed an issue where the 2D diagram colors did not render correctly.

DSC-31834– Reduced the memory consumption of the Ligand Profiler protocol. A higher consumption was only noticeable when running a very large number of pharmacophores.

DSC-31840– Fixed an issue with the Dock Ligands (CDOCKER) protocol where a docking run in non-parallel mode using a large data set resulted in a memory usage spike.

DSC-31857– Added information to the documentation about running the Flexible Docking protocol with a large number of flexible residues.

DSC-31863– Improved the Analyze Trajectory protocol reporting to reduce high memory usage.

DSC-31951– Fixed an issue in the Analyze Trajectory protocol to allow the Trajectory File parameter to read a dcd file from the Pipeline Pilot client.

DSC-31972– Fixed an issue with the Common Feature Pharmacophore Generation protocol that allowed you to set the Scale Feature Blob Size to an invalid value of 0.

DSC-31975– Fixed an issue where the Ligand Pharmacophore Mapping protocol incorrectly reported success when no hits were found. It now reports an error for those cases.

DSC-32002– Discovery Studio Client 2D structure diagrams now display double-bond stereochemistry correctly.

DSC-32007– The Atom Selection parameter values in several CNX protocols now only include valid CNX values.

DSC-32180– Fixed an issue in the Analyze Protein-Ligand Complexes example protocol so that multiple proteins can be specified for analysis. The user interface of the protocol has been redefined with some parameter name changes. Note that the Protocol.pr_xml file is not backward compatible.

DSC-32210– Fixed issue that prevented the Generate Ligand Pairs for FEP protocol from running successfully when the Lead Ligand Name parameter was blank.

DSC-32274– The Discovery Studio Files Explorer now reports the sizes of large files (>2GB) correctly.

DSC-32279– Fixed an issue in the Loop Refinement protocol. A loop including the residue before the c-terminal residue is now valid input.

DSC-32354– CHARMm memory usage is reduced for solvated systems with greater than 45,000 atoms.

DSC-32548– Fixed an issue where the Ligand Profiler protocol allowed multiple inputs from the Input File Pharmacophores, Input LigandProfilerDB Pharmacophores, and Input PharmaDB Pharmacophores parameters, but only used one of the inputs at a time. Now only a single input is allowed per run.

DSC-32578– Changed the database name pat to pataa in the BLAST Search (NCBI Server) protocol to conform with the database name change from NCBI.

DSC-32668– Fixed an instability issue in the Discovery Studio Client when docking/undocking the Molecule Window.

DSC-31353– The Prepare Proteins protocol now correctly ignores Loop Definition when the Build Loops parameter is set to False.

DSC-31814– The BIOVIA_2020.BLASTDB_README.txt files are no longer needed and the BLAST databases are part of the Discovery Studio server installer. See DSC-32218 for more detail.

DSC-31820– The Atom Element scripting API now returns "F" instead of "Fl" for Fluorine.

DSC-31876– The random number information was removed from the charmm.log file for Dock Ligands (CDOCKER) protocol.

DSC-31999– The choices presented with Amino Acid at Terminus and Mutate Amino Acid in the Edit X-ray Structure tool panel no longer depend on whether a 3D structure has been loaded into the Discovery Studio Client.

This release of BIOVIA License Pack includes the following fixed defects.

LPK-562– Security vulnerabilities in FlexNet License Server libraries used in the BIOVIA License Pack have been addressed by upgrading them to FlexNet 11.16.6.

LPK-493– Fixed an issue that caused lp_profile to generate repeated output.

Resolution

BIOVIA Discovery Studio 2021 Golden was released in December 2020 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: 2021

Level: BIOVIA 2021 Golden

How to contact BIOVIA Support

If you have any questions, please contact BIOVIA Support.