Hello Community, I am evaluating whether BIOVIA Discovery studio can support an integrated workflow for studying biomolecular interactions in a realistic membrane environment. My actual query is, can binding affinity, molecular dynamics, and interaction analysis be performed for a membrane-embedded receptor within a lipid bilayer, including its interactions with small-molecule ligands, and can the dynamic behaviour of ion-oxidized nanoparticles interacting with this membrane system also be

BIOVIA Direct 2026 HF1 was released on January 21, 2026 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 2026 Level: BIOVIA 2026 Golden Fixes for this level: BIOVIA 2026 Golden HF1 The following Technical Note informs you about BIOVIA Direct 2026 HF1 including the release's supported operating systems, enhancements and fixed defects.

Since Discovery Studio 2026 users can both read and write .cif files in addition to PDB files. If you are not familiar with cif files: The CIF (Crystallographic Information Framework), specifically mmCIF (macromolecular CIF), is the modern, official standard for the Protein Data Bank (PDB), replacing the legacy PDB file format (.pdb). While the PDB format was dominant for decades, its rigid 80-column structure cannot handle the large, complex molecular structures (like ribosomes or large

I am using Build Homology Model to complete the 3D structure of a zinc finger protein by copying from a template an experimentally determined protein region (NMR structure from the PDB) that contains the zinc finger. The resulting model is geometrically correct; however, when I run Prepare Protein (even after performing minimization and protein preparation), the zinc finger is not handled correctly. In contrast, in the experimental PDB structure, Prepare Protein assigns correct parameters and

Hi all, I have a list of ligand to be prepared generating tautomers, isomers and such. All the ligands have 3 stereocenters, but I want to keep fixed 2 and let the remaining one to be R or S. It is not completely clear to me the options in the tool "Prepare Ligands" Thanks in advance. Andrea

PURPOSE: This script is used to convert output poses generated by GOLD docking to individual PDB files each containing one protein-ligand complex. If flexible receptor atoms are incorporated in the docking these will be saved in the individual PDBs. The output pdb files are written to the directory specified in the $JobDir parameter below. INSTALLATION: Unzip and save ConvertGOLDdockingPoses2PDB.pl to a local directory or location accessible from the Files Explorer USAGE: From DS Client,

Hi, I want to export data of ELNs from Biovia to be extracted and sent to some Data Lake for building a Data Platform. Is there any way to integrate this via some API or pushing data to Amazon S3 bucket or Azure. What are my options ? Thanks

I just updated to a new laptop (Dell with 32GB RAM, AMD Ryzen, AMD Radeon Graphics) and installed the free version of DS2025. I previously was running DS2019 on an older Dell (8GB, Intel chip set). Created a lot of dsv files on the old laptop - all open just fine on new laptop, but now my pointer is misaligned with the structures - selecting atoms of a ligand in a crystal structure is essentially impossible - the pointer is low and to the right of where it appears to be on the screen. Is this

Dear BIovia Discovery Studio Community, I am writing to kindly ask for your help regarding an issue I encountered when restarting a molecular dynamics simulation in Discovery Studio. Due to an unexpected power outage, I had to stop a running dynamics simulation that was launched using Dynamics (Production). Following the official Discovery Studio tutorial, I attempted to restart the simulation from the point where it was interrupted. In particular, I followed these steps: To continue the

Dear BIOVIA Community, I have a question regarding trajectory analysis. I extended the simulation time of a molecular dynamics run by restarting the dynamics using the restart file (.rst) from the penultimate simulation, keeping the same initial conformation. In the end, I would like to analyze the full trajectory of the entire simulation, including all frames from all the dynamics runs. However, when I load only the .ene and .dcd files from the last dynamics run, the analysis includes only the

Hi all, in the Calculate Binding Energy protocol I cannot understand how to define the flexible portion of the receptor by managing the following parameters: Flexible Receptor Atom PropertySphere of Flexible AtomsFlexible Residues Thank you in advance, Andrea

Hi all, I selected a CDocker protocol as best solution for starting poses generation (according to my receptor-ligands system), but I would like to consider also the flexibility of some receptor residues, to improve this results. I saw the Flexible Docking protocol, but this generates the starting pose by LibDock (that I prefer to avoid). Any suggestions or useful hints from your side? Thank you in advance. Best regards, Andrea

Hi everyone, I am studying a system composed by a big size protein (Integrins family) complexed with small molecule candidates, trying to obtain a ranking of binding free energies. The receptor site is enough exposed and I suppose that the ligands (very flexible) could adopt different poses within the binding site. I would like to approach these kind of systems by dynamics calculations: what about using GAMD for this task? I saw some references where the ligand binding is studied with GAMD

Hello, I’m currently developing a module for Discovery Studio and have noticed that the integrated HTML viewer seems to use a relatively basic rendering engine. It may not fully support modern HTML, CSS, and JavaScript features that are commonly handled by contemporary browsers like Chrome or Chromium. Are there any recommended solutions or workarounds to improve compatibility with modern web content?

Hi, all Molecular dynamics simulations require appropriate protonation states for both the protein and the ligand. Recently, I plan to use LiGaMD to simulate the dissociation process of the protein–ligand complex. Since LiGaMD is only available through the AMBER software package, I would like to know how to prepare protonated structures of the protein and ligand such that they are compatible with AMBER. Halen

I simulated the protein–ligand complex using AutoDock Vina, and the final output was analyzed for interactions. The complex was converted to PDB format using PyMOL, and the saved PDB file was then visualized in BIOVIA Discovery Studio to generate 2D interaction diagrams. However, I encountered issues during interaction analysis: hydrogen-bond interactions observed in the 3D view (in PyMOL) do not appear in the 2D interaction diagram in Discovery Studio. In addition, some double bonds in the

This section of the wiki is all about add-ins that have been written for BIOVIA Draw. The BIOVIA Draw application comes with a feature filled .Net API that allows extension of the application's feature set with add-ins written in .Net (C# or VB). The add-ins listed are freely available upon request and demonstrate what's possible. If you are a user of the Chemical drawing package BIOVIA Draw, or are looking to purchase: you may find this FREE library of add-ins interesting/useful. BIOVIA Draw

Dear [Team/Support], I am working with a system composed of several amino acids and I need to run molecular dynamics using the Production (Dynamics) option in Discovery Studio. Both the protein preparation and solvation steps complete successfully; however, when I launch the Standard Dynamics Cascade, I encounter the following error: 09-Dec-2025 16:44:35 HTTP request 'https://urania:9943/jobs/5FC4FB2B-5881-A84C-8F1D-D263CA39A9F2/results' to server 'urania' failed. 500 - Internal Server Error

BIOVIA Discovery Studio 2026 was released in November 2025 and is available for download at https://software.3ds.com under BIOVIA products: Product line: Lab, Scientific and Content Solutions Release: BIOVIA 2026 Level: BIOVIA 2026 Golden Fixes for this level: N/A The following Technical Note informs you about BIOVIA Discovery Studio 2026 including the release's supported operating systems, enhancements and fixed defects. How to contact BIOVIA Support If you have any questions, please contact

BIOVIA Chemical Registration 2026 was released on November 28, 2025 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 2026 Level: BIOVIA 2026 Golden The following Technical Note informs you about BIOVIA Chemical Registration 2026 including the release's supported operating systems, enhancements and fixed defects.

BIOVIA Biological Registration 2026 was released on November 28, 2025 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 2026 Level: BIOVIA 2026 Golden The following Technical Note informs you about BIOVIA Biological Registration 2026 including the release's supported operating systems, enhancements and fixed defects.

On 28 November 2025, BIOVIA released BIOVIA Direct version 2026. As listed in the Product Release Document for Direct 2026, this version includes 11 new scientific calculators (DIR-4512 to DIR-4522) as well as changes and improvements to existing functions (DIR-4272 and DIR-4407). The documentation on these enhancements is not yet complete in the original Direct 2026 release. Additionally, in the original Direct 2026 release, substructure searches with molecules with enhanced axial

BIOVIA Direct 2026 was released on November 28, 2025 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 2026 Level: BIOVIA 2026 Golden The following Technical Note informs you about BIOVIA Direct 2026 including the release's supported operating systems, enhancements and fixed defects.

Dear Community I am writing to request assistance with an issue I am encountering when running a production molecular dynamics simulation with NAMD using BIOVIA Discovery Studio. My system consists of a protein of many aminoacids. I perform the full workflow in Discovery Studio, including protein preparation and minimization, followed by the Standard Dynamics Cascade using implicit solvent. The entire cascade completes successfully. However, when I attempt to start the NAMD production run using

TechNote Reference: https://www.3ds.com/support/documentation/t46-2025-biovia-pipeline-pilot-licensing-file-format-change-release-2026 Technical Note T46-2025 December 2025 BIOVIA Pipeline Pilot: Licensing File Format Change in Release 2026ProgramBIOVIA Pipeline Pilot and any BIOVIA Product with Pipeline Pilot dependency. Operating SystemAll supported operating systems BackgroundAs part of BIOVIA Release 2026, we have made changes to our license format for Pipeline Pilot and associated

BIOVIA BIOVIA Draw 2026 was released in November 2025 and is available for download at https://software.3ds.com under BIOVIA products: Product line: Lab, Scientific and Content Solutions Release: 2026 Level: BIOVIA 2026 Golden Fixes for this level: N/A The following Technical Note informs you about BIOVIA BIOVIA Draw 2026 including the release's supported operating systems, enhancements and fixed defects. https://www.3ds.com/support/documentation/t49-2025-notification-regarding-biovia-draw-2026

Hello everyone, I am reaching out because I am having trouble installing the Discovery Studio software. I attempted to perform molecular docking using the software. However, I have been unable to install it properly. When I launch the installation package you provided, the process starts but then stops unexpectedly. Could you please assist me with this issue? It's very important for my work.

Big fan of visualizer, Wondering if the development team has for adding more current 3D model export options, or user scripts? perhaps one of these: VRML2, USD (universal scene description) OBJ, FBX?

PURPOSE: Calculates the fraction of sp3 carbons in a molecule. Fsp3 = number of sp3 hybridized carbons/total carbon count. INSTALLATION: Unzip the attached file and save CalculateFsp3.pl to a local directory or location accessible from the DS Client Files Explorer USAGE: In the DS Client open CalculateFsp3.pl. Or from the DS Client's Files Explorer, right-click on the CalculateFsp3.pl file and select Open With | Script Window then launch the script using the Run command from the Scripting

ProgramBIOVIA Direct (all versions) Operating SystemAll supported Linux versions DescriptionBIOVIA Direct consists of a library that extends Oracle with the capability to store, search and retrieve chemical structures and reactions. To make the library available to Oracle, BIOVIA Direct requires the configuration of an Oracle extproc listener. On the Linux platform, you can configure the extproc listener to run from an operating system account with limited permissions. The chapter "Prepare

PURPOSE: Copies the values of the calculated ESP_Charges_DMol3 charges into the Partial Charge property. INSTALLATION: Unzip the attached file and save ChangePartialChargeForDMOL3Charge.pl to a local directory or location accessible from the DS Client Files Explorer USAGE: In the DS Client open ChangePartialChargeForDMOL3Charge.pl. Or from the DS Client's Files Explorer, right-click on the ChangePartialChargeForDMOL3Charge.pl file and select Open With | Script Window then launch the script using

Dear my colleagues: Would there be a good way to apply QM charges (like ESP charges) to a small molecule, evaluated using Small Molecules > Calculate Molecular Properties, as a Density Functional QM Properties? I successfully evaluated ESP_Charges_DMol3, and I would like to update the Partial Charge column of the resulting structure with the information. I tried copy-and-pasting the ESP_Charge_DMol3 column onto Partial Charge column, but it did not work. I pasted the contents in Excel, removed

BIOVIA is announcing the discontinuation of development of the on-premise Discovery Studio Linux client. Users will be able to use the Windows client in place of the Linux client. The Linux server will continue to be supported and is not affected by this decision. The Discovery Studio 2025 SP1 (June 2025) release is the last release that includes a Linux client. Dassault Systèmes BIOVIA remains resolutely committed to Discovery Studio, and will continue to provide new science, functionality and

A comprehensive resource for exploring the BIOVIA portfolio's capabilities can be found in our blog posts. You can access these by visiting https://blog.3ds.com/brands/biovia/.

One available feature in Discovery Studio are the Example Protocols. These protocols add functionality to Discovery Studio and they range from Simulation tools, Macromolecule tools to Pharmacophore. Some examples are Simulated Annealing, and Calculate Binding Energies with MM-PBSA, amongst others. To take advantage of these protocols you need to make the Protocols Explorer visible by navigating to View > Explorers and toggling on "Protocols".

BIOVIA Draw 2025 SP1 was released in July 2025 and is available for download at https://software.3ds.com under BIOVIA products: Product line: Lab, Scientific and Content Solutions Release: 2025 Level: BIOVIA 2025 Refresh2 Fixes for this level: BIOVIA 2025 Refresh2 The following Technical Note informs you about BIOVIA Draw 2025 SP1 including the release's supported operating systems, enhancements and fixed defects.

Hello, There will be two complimentary workshops hosted by BIOVIA product experts at BIOVIA Live 2025, taking place in Dublin, Ireland, October 6–8. WorkshopTimeInstructor(s)AbstractRegisterProtein Binder Design: From Target Assessment to AI-driven GenerationMonday, October 6 10:00 AM – 12:00 PM @AC & @AG Use Discovery Studio’s integrated workflow to analyze the structural and biophysical properties of protein targets, then generate and optimize novel binders with deep learning models

Dear all, I am in a situation where I need to save each ligands profiled by CDOCKER protocol in individual pdb files with their associated receptor protein. I am working with Discovery Studio. Is there any way to automate this process ? Thanks for your help !

Hi all, in the framework of Discovery Studio, I would like to have a more detailed and clearer (with respect to help) information about the chemical space covered by the compounds/fragments libraries integrated in the software. Can someone help me? Thanks in advance, Andrea

Hi All, I am a regular user of BIOVIA Discovery Studio and have been using the software for quite some time. I have a general query regarding the parameters used for identifying non-bonded interactions in protein–ligand complexes. Specifically, I would like to know the default distance and angular criteria used by Discovery Studio for classifying common non-bonded interactions such as: Hydrogen bonds (e.g., donor–acceptor distance and angle range) Pi–Pi interactions (e.g., centroid–centroid

Hello, I am a master's student living in Turkey. I would like to use a figure showing ligand–protein interactions generated in the free version of Discovery Studio in my thesis by taking a screenshot and citing it as a reference. Is this legally permitted?

BIOVIA Discovery Studio 2025 SP1 was released in June 2025 and is available for download at https://software.3ds.com under BIOVIA products: Product line: Lab, Scientific and Content Solutions Release: BIOVIA 2025 Level: BIOVIA 2025 Refresh2 Fixes for this level: N/A The following Technical Note informs you about BIOVIA Discovery Studio 2025 SP1 including the release's supported operating systems, enhancements and fixed defects. How to contact BIOVIA Support If you have any questions, please

Hi all, concerning DFT calculations in DiscoveryStudio, is it possible to increase the SCF_iterations number (over 50)? Thanks in advance Andrea

Hello all, I have a huge ligand library that I have screened using LibDock. Now I want to perform docking (using CDocker) for my top 10 molecules. I get the error 'no refined poses found for ligand'. I have tried changing the parameters in Cdocker, increasing binding pocket area, yet no results. Kindly help!

Hi, I’m using DS 2025 and successfully created a 3D database using the "Create 3D Database" tool. However, when I try to search the generated database using the "Search 3D Database" tool, I encounter a system error with the message: "Unable to upload fileC:\Users......." Has anyone experienced this issue or knows how to resolve it? Thanks in advance for your help!

ProgramBIOVIA Direct (all versions) Operating SystemMicrosoft Windows Server (as supported by the installed BIOVIA Direct version) SummaryAs previously reported this post again points out a problem with the Oracle 19c Database Bundle Patches 19.24, 19.25, and 19.26 which leads to malfunction of all BIOVIA Direct versions in use. The problem manifests itself in the fact that an Oracle error "ORA-28576: lost RPC connection to external procedure agent" regularly occurs when calling Direct

I've installed BIOVIA Discovery Studio on several computers in the past, but this is a new issue I've encountered: Steps to produce issue: I download and run BIOVIA_DS2024Client.exe During the installation of the BIOVIA License Pack 2024, the InstallShield Wizard triggers a popup window which states "The system cannot open the device or file specified.". The popup window has two options: Retry and Cancel. Clicking "Retry" just triggers the same popup window. Clicking "Cancel" and proceeding with

Hi all As the question described, such as 5P9J and 6YG2. How can I assign the charmm36 forcefiled successfully using Assgin Forcefiled protocol.

The Measure Trajectory Features protocol is useful for measuring molecular dynamics time-series features such as root-mean-square distance from a reference conformation (RMSD), solvent-accessible surface area (SASA), dihedral angles (Dihedral), and intermolecular or intramolecular distances between nearest atoms of residues (Distance). The required parameters are an Input Molecule (i.e. a .dsv file loaded into the DS Client) and and Input Trajectory (a corresponding .dcd file containing the

I am using liganProfiler to identify potential targets from the PharmaDB database. The results are provided with a FitValue score. Does this depend on a number of pharmacophore features? I am curious to know how this FitValue is calculated. The help document does not provide any detailed descriptions of the parameters used for calculating the FitValue score except for the sentence, "A measure of how well the ligand fits the pharmacophore. The higher the fit score, the better the match." Also,

Hello, my company needs to install this program at an Enterprise scale, but we can't figure out how to silently install it. Our users don't have admin permissions so this is our best way to deploy it. Does anyone have any tips?

In case you missed this virtual event last week, you can watch the replay here: Agenda: Designing Novel Molecules Against Pathogenic Bacteria with Machine Learning and Molecular Modelling + Q&A Rupesh Chikhale, PhD, Cambridge Crystallographic Data Centre Retrosynthesis for the Medicinal Chemist Alexandre Cabaye, PhD, BIOVIA In Silico Design of Multi-Specific Protein Therapeutics Mahiuddin Ahmed, PhD, VITRUVIAE OpenFold Consortium: The Development of OpenFold3 + Q&A Lucas Nivon, PhD, Cyrus

Are you looking to gain a deeper understanding of protein formulation and its critical role in antibody design? Don't miss out on our upcoming webinar on protein formulation design using Discovery Studio Simulation. Webinar highlights: • Learn how to predict protein aggregation, viscosity, and solubility. • Discover effective strategies for optimizing excipient in protein formulation. • Explore techniques to enhance protein stability for formulation design. Live webinar: Tuesday, August 21 |

What’s Gaussian accelerated molecular dynamics (GaMD) and how can it provide insights into peptide folding or antibody binding? Join the webinar by Dr. Reed Harrison on Wednesday, September 6th to explore how this enhanced sampling technique can help study the molecular behavior of biological systems. 👉 Check out the agenda and register here: https://events.3ds.com/discovery-studio-simulation #DiscoveryStudioSimulation #GaMD #MolecularDynamics #ModSim

Here is a link to our webinar recoding for those who have missed it: https://events.3ds.com/discovery-studio-simulation-antibody-formulation

Speed up discovery with cutting-edge science on the 3DEXPERIENCE platform: https://blog.3ds.com/brands/biovia/elevating-excellence-in-drug-discovery-combining-ai-ml-models-with-physics-based-simulation-methods-in-discovery-studio-simulation. 🎉 Google DeepMind’s AlphaFold2 and OpenFold AI models are now available in BIOVIA Discovery Studio Simulation on the 3DEXPERIENCE platform, enhancing the power of physics-based molecular modeling and simulation with deep learning.

BIOVIA provides researchers with advanced, end-to-end business solutions on a single cloud-based platform, to support small molecule therapeutics design. The 3DEXPERIENCE platform also improves collaboration across cross-functional teams within the organization or among networked partners: 🧬 BIOVIA Generative Therapeutics Design – Generate ideas for which compounds to make next with AI and machine learning 🌐 BIOVIA Discovery Studio Simulation – Accelerate life sciences research with a

Our latest insights reveal the synergy between open-source flexibility and commercial reliability. Discover how BIOVIA Pipeline Pilot is transforming the field by seamlessly integrating robust commercial workflows with the power of Python. This allows our scientific community to harness the best of both worlds, significantly boosting efficiency and productivity. Dive into the latest blog by Dr. Chitral Naik, our Director of Portfolio Strategy, for a comparison and see how we're bridging the gap

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Hi everyone, I’m analyzing protein–ligand interactions and used Discovery Studio Visualizer (DSV) to identify various non-covalent interactions, such as π–π stacking, cation–π, and π–alkyl interactions. I would like to understand how these interactions are calculated in structural terms. For example, in the case of π–π stacking, are there specific distance and angular criteria (e.g., centroid–centroid distance between aromatic rings and the angle between their normal vectors) that are typically

Dear Discovery Studio experts: A customer wants to find a way to refine CDOCKER result with detailed interaction analysis. The ligands are peptides or oligonucleotides. Because of their shear length, they interact with residues outside of binding pocket (active site) of a protein, and CDOCKER energy is not a reliable index for them. I guess the Simulation > Analyze Trajectory > Analyze > Calculate Interaction Energy protocol might be an answer. A binding pocket group should be defined first,

In an article published last year in the Journal of Chemical Information and Modeling, scientists lead by Anne Goupil-Lamy presented a computational method to identify the epitope of a rat mGlu5 receptor nanobody. Throughout their study, the authors employed Discovery Studio 2022 in multiple stages, including model generation, rigid protein-protein docking, molecular dynamics, binding mutation energy calculations, and aggregation propensity score assessments. Initially the authors generated

Hello, I am trying to use the BIOVIA discovery studio to visualise the ligand-protein interactions, but when uploading my file to the software, my ligand fragments and will not show the 2d sequencing. I sent a colleague the same file, and it worked fine (1st picture attached). Any suggestions why the software isn't uploading the ligand properly (2nd picture)? I have tried deleting and reinstalling and also starting from scratch with regard to the structure and binding affinities obtained in

Dears I’m currently exploring the Discovery Studio Simulation within the 3DEXPERIENCE SaaS cloud platform, and I had a couple of questions that I was hoping you could help clarify. Does the Discovery Studio Simulation in 3DEXPERIENCE use AWS cloud servers for its operations? What type of hardware, such as CPU and GPU, is typically utilized for running calculations in the SaaS Cloud? Has anyone compared the simulation speed between on-premise setups and the cloud version, particularly in terms of

Is it possible to make the protein (solid ribbon) display style translucent? If so, please let me know how to do this. Additionally, I would like to know how to change the color of individual amino acid residues. Please let me know how to do that.

The latest version of the free Discovery Studio Visualizer can be downloaded from: https://discover.3ds.com/discovery-studio-visualizer-download-thank-you Simply fill in a few fields and gain access to either the Windows or Linux installer.

if i can install Biovia 2025 licensed version on CentOS 9 ? any idea about this. or cent os 8 is only compactable?

ProgramBIOVIA Direct (all versions) Operating SystemAll supported operating systems SummaryBIOVIA has internally observed that after applying Oracle 19c Release Update 24 (aka Oracle 19.24.0.0.0) installed BIOVIA Direct versions may no longer work. Calls to BIOVIA Direct operators, functions and procedures then fail with the Oracle error ORA-28576: lost RPC connection to external procedure agent. The problem apparently only occurs with a small number of patch installations. Linux and Windows