BIOVIA DISCOVERY STUDIO® 2021
COMPREHENSIVE MODELING ANDSIMULATIONS FOR LIFE SCIENCES
DatasheetDELIVERING NEW SCIENCE
Molecular simulations are essential to modeling and understanding complex biomolecular systems. The latest release of BIOVIA’s
predictive science application, Discovery Studio®, improves theMulti-Site Lambda Dynamics workflow and accelerates science
with more GPU-enabled platforms. Built on BIOVIA Pipeline
Pilot™, Discovery Studio® is uniquely positioned as the mostcomprehensive, collaborative modeling and simulation application for Life Sciences discovery research.

DISCOVERY STUDIO 2021
Part of the 2021 BIOVIA product release series, Discovery Studio
2021 continues to deliver scientific developments in the areas ofbiotherapeutics, simulations and small molecule research.

NEW AND ENHANCED SCIENCE

New! Free Energy Perturbation with CHARMm-DOMDEC.
• A new CHARMm Relative FEP Calculations protocol allows
FEP calculations of multiple systems on GPU (Linux).
• Forward and Reverse estimates of free energy.
• Custom lambda schedule with narrower windows near the end
states to improve accuracy.
New and Enhanced! Atom typer and force field parameters.
• More accurate and consistent small molecule hierarchical atomtyping scheme with CGenFF.
• Extended and improved force field bond and angle parameters,
significantly expanding CGenFF chemical space.
Enhanced! Viscosity and Aggregation prediction for biologics.
• Calculate Protein Formulation Properties protocol automaticallygenerates Charge Map3 and Aggregation Scores3 surfaces.

New! Multi-Site Lambda Dynamics1 workflow.
• A single protocol, MSLD Bias Optimization and Production,
combines three protocols for a simplified and enhanced userexperience with CHARMm on GPUs.
• Calculate relative binding free energies for an entire combinatorial library in a single simulation, mimicking a competitive
binding assay.
• Large scale2 validation establishes the accuracy of the science
to explore large congeneric chemistry space in early lead
optimization.
• Up to 20 times more efficient than FEP.

Figure 2: Charge QMap (left) and Aggregation Scores (right)
surfaces on an antibody structure.

Enhanced! Various protein modeling enhancements.
• RCSB Structure Search: Rewritten to support new JSON queries, as previous search APIs were retired November 2020.
• BLAST Search (NCBI Server): Improved performance androbustness.
• Analyze Protein-Ligand Complexes: Allows multiple proteinsas input.
• Predict Humanizing Mutations: Improved performance andloads germline files more easily.
• Retrieve Antibody Templates from Database: New example
protocol available to retrieve specified antibody templates fromthe database.
Figure 1: MSLD validation2 with seven protein targets and 165
ligands, with average unassigned error (AUE) = 0.76 kcal/mol.

• BLAST PDB and Swiss-Prot databases automatically installed.

Enhanced! Various pharmacophore modeling enhancements.

PARTNER SCIENCE• CHARMm: Incorporates the latest release of the academic
CHARMM, version c44b25.

• Non-bond pharmacophore features supported in the ligandbased pharmacophore protocols, and the Edit and Cluster
Features tool panel.

• NAMD: Distributed with both CPU and GPU editions, version 2.13.

• PharmaDB scPDB receptor-ligand targets updated with nonbond pharmacophore features.

• MODELER: Incorporates the latest release of the academic
MODELLER, version 9.246.

• Full PharmaDB database now included in default installation;
the disk space has reduced from ~10 GB to 0.27GB.

• BLAST+: The BLAST+ version in Discovery Studio has been
updated to version 2.10.1.

4• GOLD: Supports GOLD 2020.

COMPATIBILITY
Discovery Studio 2021 is built on BIOVIA Pipeline Pilot 2021.

DATABASES• The ANTIBODY database has been updated to include thelatest antibody template structures from the PDB (based onPDB release July 2020).
Figure 3: Interactions pharmacophores harmonize with
non-bond feature perception.

New! GPU- enabled protocols to accelerate calculations.
• Dock Proteins (ZDOCK): Up to 13x faster than CPU.
• Dynamics (NAMD) and Solvate with Explicit Membrane:
1 GPU is 7-10x faster than 8 CPUs.
• MSLD Bias Optimization and Production: Runs on both gridand non-grid servers.
• CHARMm Relative FEP Calculations (GPU): FEP Calculations now supported with DOMDEC-GPU.

Figure 4: Performance improvements of 2021
GPU-enabled protocols relative to 2020 CPU versions.

• PDB and PDB_nr95 BLAST databases have been updated(based on PDB data July 2020).
• Swiss-Prot BLAST database has been updated (based onUni-Prot from July 2020).
• The RCSB Structure Search protocol ligand database has
been updated (July 2020, 32,522 entries).

REFERENCES
1.

Hayes R. L., Armacost K. A., Vilseck J. Z., Brooks III C. L.,
J Phys Chem B., 2017, 121, 3626-3635.

2.

Raman E. P., Paul T. J., Hayes R. L., Brooks III C. L., J Chem
Theory Comput., 2020, 16, 7895–7914.

3.

Agrawal N. J., Helk B., Kumar S., Mody N., Sathish H. A.,
Samra H. S., Buck P. M., Li L., Trout B. L., MAbs., 2016; 8,43-8.

4.

http://bioinfo-pharma.u-strasbg.fr/scPDB/

5.

Brooks B. R., Brooks III C. L., Mackerell A. D., Karplus M., etal, J. Comp. Chem., 2009, 30, 1545-1615.

6.

Eswar N., Marti-Renom M. A. Webb B., Madhusudhan M. S.,Eramian D., Shen M., Pieper U., Sali A., Current Protocols in
Bioinformatics, John Wiley & Sons, Inc., 2006, Supplement
15, 5.6.1-5.6.30.

©2020 Dassault Systèmes. All rights reserved. 3DEXPERIENCE, the Compass icon, the 3DS logo, CATIA, BIOVIA, GEOVIA, SOLIDWORKS, 3DVIA, ENOVIA, EXALEAD, NETVIBES, MEDIDATA, CENTRIC PLM, 3DEXCITE, SIMULIA, DELMIA, and IFWE are commercial trademarks
or registered trademarks of Dassault Systèmes, a French “société européenne” (Versailles Commercial Register # B 322 306 440), or its subsidiaries in the United States and/or other countries. All other trademarks are owned by their respective owners. Use of any Dassault
Systèmes or its subsidiaries trademarks is subject to their express written approval.Ò

Our 3DEXPERIENCE® platform powers our brand applications, serving 11 industries,and provides a rich portfolio of industry solution experiences.
Dassault Systèmes, the 3DEXPERIENCE Company, is a catalyst for human progress. We provide business and people with collaborative
virtual environments to imagine sustainable innovations. By creating ‘virtual experience twins’ of the real world with our 3DEXPERIENCE
platform and applications, our customers push the boundaries of innovation, learning and production.
Dassault Systèmes’ 20,000 employees are bringing value to more than 270,000 customers of all sizes, in all industries, in more than 140
countries. For more information, visit www.3ds.com.

Europe/Middle East/Africa
Dassault Systèmes
10, rue Marcel Dassault
CS 40501
78946 Vélizy-Villacoublay Cedex
FranceAsia-PacificDassault Systèmes K.K.
ThinkPark Tower
2-1-1 Osaki, Shinagawa-ku,
Tokyo 141-6020
Japan

AmericasDassault Systèmes
175 Wyman StreetWaltham, Massachusetts
02451-1223
USADS-9935-0121