® BIOVIA DISCOVERY STUDIO 2019 COMPREHENSIVE MODELING AND SIMULATIONS FOR LIFE SCIENCES Datasheet RUNNING SIMULATION ON GPU Molecular simulations are essential to modeling and understanding complex biomolecular systems. The latest release of BIOVIA’s predictive science application, Discovery Studio®, introduces the first implementation of CHARMm GPU via an OpenMM interface for highly optimized and efficient molecular dynamics simulations. Built on BIOVIA Pipeline Pilot™, Discovery Studio® is uniquely positioned as the most comprehensive, collabora- tive modeling and simulation application for Life Sciences discovery research. DISCOVERY STUDIO 2019 • Antibody Modeling Cascade: Residues in predicted structures Part of the 2019 BIOVIA product release series, Discovery Studio numbered in accordance with the antibody annotation 2019 continues to deliver key new small molecule research, scheme. simulations and antibody humanization enhancements. • Antibody Modeling Cascade: Annotated alignment of the sequences linked to the modeled structures is displayed. NEW AND ENHANCED SCIENCE • Protein Ionization and Residue pK: The protocol can take New! CHARMm GPU support via OpenMM interface multiple proteins as input and the calculation of solvation for running molecular dynamics simulations energy term is significantly faster. • OpenMM GPU provides a highly optimized performance and cost effective solution for running molecular simulations. • Compared to the highly parallelized NAMD CPU, CHARMm- OpenMM running on one GPU is approximately 9 times faster than NAMD on an 8 core CPU. • Dynamics (Production): Added options in this protocol to support GPU for Linux platform. GPU vs CPU Performance 80 60 y a d / 40 ns 20 0 Figure 2. Annotated alignment and model 25K Atoms 35K Atoms 61K Atoms structures generated by Antibody Modeling CHARMm CPU8 NAMD CPU8 CHARMm-OpenMM GPU Cascade. Figure 1. Performance comparison of New! New protocol, Analyze Crystal Contacts, to CHARMm-OpenMM GPU against CHARMm generate and analyze crystal contacts and NAMD CPU using non-bond list cutoff • Rapidly generate symmetry-related copies around the of 14 Angstrom for 3 molecular systems. asymmetric unit of a PDB crystal structure. • Identify contact residues by comparing residue solvent accessible surface areas in the isolated molecule and the Enhanced! Grid support for simulation protocols crystal form, and distinguish contact residues by color. • Dynamics (Production): CPU resources for running CHARMm MPI and GPU resources can be requested on a grid engine • Find and display non-bond interactions between the original through the queuing system. molecule and the symmetry copies. Optionally, find bridging water interactions involving symmetry copies. • Dynamics (NAMD): CPU resources for running NAMD multicore can be requested on a grid engine through the Enhanced! queuing system. • Ligand Pharmacophore Mapping: Fit and atom contributions for mapped pharmacophore features have been added. Enhanced! • Generate Analog Conformation: Extended the protocol to Enhanced! support coarse-grained parallelization. • User preferences for surfaces can be saved. Enhanced! Various protein modeling enhancements PARTNER SCIENCE • Predict Humanizing Mutations: Simultaneously search both • CHARMm: Incorporates the latest release of the academic light and heavy chain antibody sequences for humanizing CHARMm code, version c42b21. mutations and predict the combined effect of the mutations from both chains to protein stability. • NAMD: Distributed with the CPU edition, version 2.12. • MODELER: Incorporates the latest release of the academic REFERENCES 2 MODELLER code, version 9.20 . 1. Brooks B. R., Brooks III C. L., Mackerell A. D., Karplus M., et al, J. Comp. • BLAST+: The BLAST+ version in Discovery Studio has been Chem., 2009, 30, 1545-1615. updated to version 2.7.1. 2. Eswar N., Marti-Renom M. A. Webb B., Madhusudhan M. S., Eramian D., Shen M., Pieper U., Sali A., Current Protocols in Bioinformatics, COMPATIBILITY John Wiley & Sons, Inc., 2006, Supplement 15, 5.6.1-5.6.30. Discovery Studio 2019 is built on and supports the latest release of BIOVIA Pipeline Pilot, version 2019. DATABASES • The ANTIBODY database has been updated to include the latest antibody template structures from the PDB (based on PDB release July 2018). • The RCSB ligand database has been updated for the RCSB Structure Search protocol (July 2018, 27,028 entries). Our 3DEXPERIENCE® Platform powers our brand applications, serving 12 industries, and provides a rich portfolio of industry solution experiences. Dassault Systèmes, the 3DEXPERIENCE® Company, provides business and people with virtual universes to imagine sustainable innovations. Its world-leading solutions transform the way products are designed, produced, and supported. Dassault Systèmes’ , the Compass icon, the 3DS logo, CATIA, SOLIDWORKS, ENOVIA, DELMIA, SIMULIA, GEOVIA, EXALEAD, 3D VIA, BIOVIA, NETVIBES, IFWE and 3DEXCITE are commercial trademarks or registered trademarks of of trademarks or registered trademarks commercial are BIOVIA, NETVIBES, IFWE and 3DEXCITE 3D VIA, EXALEAD, SOLIDWORKS, ENOVIA, DELMIA, SIMULIA, GEOVIA, CATIA, the 3DS logo, icon, , the Compass collaborative solutions foster social innovation, expanding possibilities for the virtual world to improve the real world. The group brings value to over 210,000 customers of all sizes in all industries in more than 140 countries. For more information, visit www.3ds.com. EXPERIENCE® 3D ©2018 Dassault Systèmes. All rights reserved. Systèmes. ©2018 Dassault or its subsidiaries Systèmes owners. Use of any Dassault owned by their respective are All other trademarks other countries. and/or States # B 322 306 440), or its subsidiaries in the United Register Commercial (Versailles européenne” “société a French Systèmes, Dassault approval. written their express is subject to trademarks Europe/Middle East/Africa Asia-Pacific Americas Dassault Systèmes Dassault Systèmes K.K. Dassault Systèmes 10, rue Marcel Dassault ThinkPark Tower 175 Wyman Street CS 40501 2-1-1 Osaki, Shinagawa-ku, Waltham, Massachusetts 78946 Vélizy-Villacoublay Cedex Tokyo 141-6020 02451-1223 France Japan USA DS-9880-0119.