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

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

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

root page for blogs

root page

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

Hello everyone, I'm running Dynamis(NAMD) with GPU on a Windows machine with an Intel Core i7-13700 and an NVIDIA RTX A5000. While using all 24 CPU threads, I notice that my GPU usage stays around 30%. Does anyone have suggestions for optimizing GPU usage in NAMD on a Windows setup? Any settings or adjustments that could increase GPU performance? Thanks in advance!

Hello everyone, I am currently studying DNA-protein complexes using Discovery Studio, and I have a few questions regarding the methods: I am using the "Prepare Protein" tool to prepare the complex. Is this approach suitable, or does Discovery Studio include a force field for nucleic acids as well? Is it feasible to perform ZDock between DNA and protein in Discovery Studio and obtain reasonable results? I would like to quantify the binding free energy between the DNA and protein. Could anyone

BIOVIA Discovery Studio 2025 was released in November 2024 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 Golden Fixes for this level: N/A The following Technical Note informs you about BIOVIA Discovery Studio 2025 including the release's supported operating systems, enhancements and fixed defects.

BIOVIA Draw 2025 was released in November 2024 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 Golden Fixes for this level: N/A The following Technical Note informs you about BIOVIA BIOVIA Draw 2025 including the release's supported operating systems, enhancements and fixed defects.

PURPOSE: Animate a trajectory and save each frame to a image file. Note the active molecule window for which frames are being saved must remain in the foreground until the script completes. INSTALLATION: Unzip the attached file and save ExportTrajectoryToImageFiles.pl to a local directory or location accessible from the DS Client Files Explorer USAGE: From the DS Client's Files Explorer, right-click on the ExportTrajectoryToImageFiles.pl file and select Open With | Script Window then launch the

PURPOSE: This script illustrates how to create a transparent ribbon. It will run on an open Molecule Window in the foreground. INSTALLATION: Unzip the attached file and save TransparentRibbon.pl to a local directory or location accessible from the DS Client Files Explorer USAGE: From the DS Client's Files Explorer, right-click on the TransparentRibbon.pl file and select Open With | Script Window then launch the script using the Run command from the Scripting toolbar. REQUIREMENTS: A molecule

PURPOSE: Uses the Minimization protocol on several input typed systems. To select several proteins on the Input Typed Molecule parameter open the dropdown menu and select Browse... Once selected a pop up will appear, here select several dsv files with typed proteins. Constrains can only be applied to all the minimized systems, no specific constrains for each system. USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in Discovery Studio,

Insight for Excel 2024 and 2024 SP1 have been tested and validated to work with Japanese Windows 11 using Microsoft Office LTSC 2019, 2021 and Microsoft Office 365, both 32 and 64bit environments. This validation is in addition to the support matrix that was approved during the 2024 and 2024 SP1 releases.

Hello again, I am trying to run steered molecular dynamics on my transmembrane protein and ligand complex. I prepared and optimized my structure, minimized it, performed docking, solvated with explicit membrane with equilibration (10 ns), ran Dynamics (NAMD) for 10 ns as well. However, my steered molecular dynamics is failing and I am getting this error: "CHARMm dynamics simulation has failed because energy change tolerance exceeded. Please ensure the initial structure is minimized and

Hello everyone! I want to calculate MMGBSAP/PBSA for my transmembrane protein-ligand complex following solvation with explicit membrane with equilibration for 10 ns and10ns of Dynamics (NAMD). I looked in the community and saw that there was a protocol posted in 2020 to do that (https://r1132100503382-eu1-3dswym.3dexperience.3ds.com/home?content=swym:prd:R1132100503382:qnaquestion:lnrXrUWCTcGLD4leymnKug&media=swym:prd:R1132100503382:media:ssBFnMMrQkys9iZRbYnZNQ) however, I am getting the

BIOVIA Direct allows, among other things, searches for molecules with an exact or a substructure formula in Oracle. For instance, a typical substructure formula search looks like this: select ID from molecules where fmlalike (ctab,'C O') = 1; The sequence 'C O' in the SQL above represents the search term for the structural formula. A common misconception is that the BIOVIA Direct search for structural formulas is a simple substring comparison. Users therefore often expect that the above

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

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?

Program All BIOVIA Applications Operating System Windows 10 Description Microsoft has announced that support for Windows 10 will end on October 14, 2025. The current version, 22H2, will be the final version of Windows 10. All editions remain in support, with monthly security update releases, until the end of support. Resolution In line with these changes, BIOVIA is clarifying the support for BIOVIA product lines: Deployments of the 2019, 2020, 2021, 2022, 2023, and 2024 releases of BIOVIA

Hi We have perpetual license for Discovery studio We are in a prosses of migrating our storage and working environment from a hard PC to Microsoft Azure cloud. Is it possible to put Discovery Studio license on Azure cloud, or it must be on hard PC? Elad

BIOVIA Draw 2024 SP1 was released in May 2024 and is available for download at https://software.3ds.com under BIOVIA products: Product line: Lab, Scientific and Content Solutions Release: 2024 Level: BIOVIA 2024 Refresh 2 Fixes for this level: N/A The following Technical Note informs you about BIOVIA Draw 2024 SP1 including the release's supported operating systems, enhancements and fixed defects.

Hi everyone, I have an error with the CHARMmRelativeFEPCalculationsGPU tool in BIOVIA DiscoveryStudio. After many hours of calculation, the work stops due to "System Error", giving this error: Authentication failed: Unable to authenticate: The user name or password is incorrect. Authentication failed connecting to 'https://xxxxxxx/security/sessions/current' CHttp::Authenticate: Pipeline Pilot exception rethrown CHttp::CheckResponseHeaderAsync: Pipeline Pilot exception rethrown

Hi, I am new to Discovery Studio. I have attempted to run a protein-ligand molecular dynamics (MD) simulation for 100 ns. However, it took a very long time and eventually ended with an error or was interrupted due to a power cut. Can anyone share their experience or advice on successfully running a 100 ns MD simulation for a protein-ligand complex?

How to perform SASA analysis after MD simulation DS?

Program BIOVIA Direct (all versions) Operating System All supported operating systems Summary For easier administration, BIOVIA Direct domain index data are partially visible to all Oracle users. The domain index data allows you to draw conclusions about the indexed original data, albeit very limited in terms of content and available time frame. This article explains the technical background and describes how you can block access to the index data and what administrative restrictions are

In the older version of DSV, to move a residue from one chain to another all I had to do was click and drag. It seems that feature has been removed and now I cannot find a way to easily edit which residues belong to which chains. Does anyone know how to do this? Or a way to get an older version of DSV?

Hello! is it possible to generate 2d interactions for DNA-ligand complexes in DS?

Last month, BIOVIA hosted its highly anticipated user meeting in Waltham, Massachusetts. The three-day in-person event brought together industry experts and thought leaders for insightful discussions and presentations on cutting-edge topics. One of the most eagerly awaited talks from the event was given by our Senior Portfolio Manager Tien Luu, PhD, where she talked about the new developments in Discovery Studio Simulation, including the out-of-the-box OpenFold/AlphaFold models available to our

hello everyone For my project ı did many docking with three ligand to proteins via Autock vina tool. And ı got results as output pdbqt and ı convert them to pdb as ı learn pdbqt not applicable for DSV. Can anyone help me how can ı automated docking results for visualization ı mainly focus creatin 2d diagram ligand receptor interaction so ı have same protocols for all results . Thank you for any kind of help .

Hi, Hope you are all doing well. I am part of a research group from UNSW, Sydney, Australia and we have a perpetual license for discovery studio. However, I have been informed the way it works is we get a code that lasts a few years and then we need a new license code to continue. Our current code expired last month and I am trying to figure out a way to get a new code, I can't find any support contacts and have been redirected here from who I could email. I would appreciate any help and/or

Hello! Is it possible to load a trajectory in the AMBER format (topology file parm7 and trajectory file NetCDF)? If so, can you play the trajectory movie like VMD/Chimera? Thank you!

Hello, I've been using Material Studio 2023 on my local computer both as a client and a server. My pc has 48 cores and I recently installed a RTX 4060 Ti and then reinstalled Material Studio 2023 but still the "use GPU" button in Forcite is not clickable. Can anyone guide me regarding how to use GPU for molecular dynamics on a local computer?