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Committed to improving research and development productivity for organizations around the world through better science and technology.

Discovery Studio & Predictive Sciences Webinars

BIOVIA Discovery Studio® software provides comprehensive modeling and simulation capabilities for computational chemists, computational biologists, and other scientists engaged in small molecule and biotherapeutics-based research. The latest release is a comprehensive product update that extends our portfolio of small molecule drug design and market-leading biological simulation tools.

We invite you to learn how the latest release of Discovery Studio helps improve efficiency and collaboration throughout your organization in this webinar series. These webinars are recommended for people familiar with Discovery Studio.

Webinars will continue to be added, please check back often.

Past Webinars

Title and Speaker

Accelerate Development, Validation and Deployment of QSAR Models
Adrian Stevens, Senior Manager of Modeling & Simulations, BIOVIA

In the past 15 years, automation in drug discovery projects led to massive increases in the amounts of data generated by multifunctional chemistry and biology teams. Data trends and patterns can help project teams make important decisions about what entity to make next in a series. The challenge is how to speed the process and reduce costs.

Developed in collaboration with GSK, the BIOVIA QSAR Workbench automates and accelerates the development, validation, deployment and life cycle management of predictive Quantitative Structure-Activity Relationship (QSAR) models. Join us to learn how to:

  • Reduce QSAR modeling time from days to hours
  • Explore and compare statistical space to identify robust, predictive QSAR models
  • Extend the reach of statistical experts

Live demos of the BIOVIA QSAR Workbench will also be shared.

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Predictive Sciences: A Transformational Opportunity For Pharmaceutical Research And Development
Dr. Chris Waller, Head of Scientific Modeling Platforms at Merck

Pharmaceutical research and development is a time- and data-intensive endeavor that requires the ability to leverage experience and knowledge in order to avoid repeating mistakes of the past, minimize late stage attrition, and help ensure that the molecules we discover and put into development become medicines.

The Predictive Sciences Program at Merck is a comprehensive package of data access, aggregation, predictive modeling, and advanced analytics that will transform productivity by releasing Merck data and the associated computational models to inform the research and development decision making processes. We anticipate a transformational step change through optimizing the use of public data, Merck data, natural language processing, and predictive models for hypothesis generation. This capability will allow scientists to use enhanced judgment in decision making, resulting in reduced attrition and cycle time and increased Merck research and development pipeline productivity. This talk will provide an update on the creation of the predictive sciences platform at Merck.

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Discovery Studio Non-Bond Analysis: Understanding Interactions
Tien Luu, Advisory Scientific Specialist, Life Science

The perception, rationalization and optimization of non-bonded interactions is one of the fundamental challenges in rational drug design. Advancing theory and new experimental evidence for molecular interactions beyond classical hydrogen bonds and hydrophobic effects have necessitated a more sophisticated and comprehensive analysis of the interactions involved in shaping and stabilizing protein conformations, protein-protein, and protein-small molecule interactions. Discovery Studio 4.0 has fully re-engineered and expanded the perception of non-bond interactions, including favorable, unfavorable and unsatisfied interactions. This webinar will present new client visualization tools to quickly and easily capture and render non-bond interactions and server components to rapidly calculate non-bond interactions for post-processing, enrichment of screening results and interaction fingerprint analysis.

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Simplifying Molecular Simulations and Analysis with Discovery Studio ®
Ken Butenhof, Senior Field Applications Scientist, BIOVIA

Discovery Studio (DS) empowers experts and non-experts with intuitive graphics interface setup and analysis for Molecular Simulations using CHARMm (MM/MD), NAMD (MM/MD), DMOL3 (DFT QM) or hybrid MM/QM methods. Multi-step commonly used workflows are greatly simplified through validated workflows (Protocols), such as the Standard Dynamics Cascade. DS Supports arbitrary chemistry (protein, DNA, carbohydrate, lipid, ligand, etc.), millions of atoms, automated residue typing, and vacuum, implicit solvent, explicit water droplet with ions, explicit solvent with ions (periodic boundary restraints/EWALD), or implicit membrane simulations. DS includes full support of multiple processors and grid engines through its robust client-server implementation based on the BIOVIA Foundation. The BIOVIA Foundation also facilitates incorporation of diverse additional functionality including but not limited to chemical informatics and advanced statistics and in addition includes a software development toolkit for incorporation of third party functionality.

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Design better biologics with improved stability and binding affinity
Lisa Yan, Senior Manager, Life Sciences R&D

Monoclonal antibody (mAB) has become an important class of biological drugs in recent years. Many of the biological and biophysical properties of protein therapeutics can be predicted based on their sequence and structure information and computational tools have been used widely in assisting antibody design in pharmatheutical industry. Discovery Studio provides well validated and comprehensive set of tools for in silico design of antibodies. It has a robust and easy to follow workflow to create antibody structures, calculates various antibody properties based on its structure, including isoelectric points, aggregation propensity and pH-dependent stability, etc. It also allows you to mutate the protein sequence and to predict the thermal stability or pH-dependent stability profile of the mutants. New tool is added to identify the possible sites to create disulphide bridges to improve protein stability. Here we will give a brief overview of the capabilities of Discovery Studio in modelling and designing anbitodies, discuss the scientific validation results of some of the methods and highlight the new functionalities and improvements in the upcoming release.

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Antibody Design in Discovery Studio 3.5
Anne Goupil, Principal Scientist

In this webinar we will present the new tools that have been implemented in Discovery Studio to work on Antibodies: numbering and alignment tools based on numbering identify Framework templates, Developability Indices calculation. We will also show some examples on how to use these tools in the Discovery Studio interface.

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New Computational Methods for Fragment Based Lead Discovery

Tien Luu

Recent developments in Fragment Based Drug Design (FBDD) have made it a promising technique for lead discovery over more traditional methods such as high throughput screening (HTS). The smaller size of fragments (molecular weight < 250 Da) allows a smaller sample of library compounds to sample a large chemical space and provide higher hit rates than screening of larger compound libraries.

In this talk, we will present a new, easy to use computational method for fragment based lead discovery. Initial fragments can either be placed using experimental methods or using the Multiple Copy Simultaneous Search (MCSS) method using CHARMm. The fragments are grown using common chemical reactions, ensuring that the generated leads are chemically tractable.

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Novel in silico prediction algorithms for the design of stable biologics

Lisa Yan, Senior Manager, BIOVIA

Understanding the effects of mutation on protein stability and protein binding affinity is an important component of successful protein design, especially in the area of protein therapeutics. In silico approaches to predict the effects of amino acid mutations can be used to guide experimental design and help reduce the cost of bringing therapeutics to market. A number of novel methods for fast computational mutagenesis of proteins have been developed and can be applied to calculate the energy effect of mutation on protein stability, and on protein-protein binding affinity with an optional pH dependency calculation. Here, we will present those methods and associated validation results. Furthermore, we will provide a case study using a set of engineered antibodies that have altered pH-selective binding. These demonstrate how binding to either neonatal receptor (FcRn) or to their target antigens can be modified to tune their half-life in the host system

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What's New in Discovery Studio 3.5

Adrian Stevens, Senior Product Marketing Manager, BIOVIA

The latest release of Discovery Studio, 3.5, is the most comprehensive modelling and simulation solution for both small molecules and macromolecules research.

This webinar will provide an overview of the new scientific functionality available in the latest release, including new market-leading tools to calculate Antibodies Developability Index, new pH-dependent mutation energy algorithm for protein-protein binding, updated techniques for modelling antibody loops and annotating antibody sequences.

In the small molecules domain, we will showcase a brand new and peer-review validated ligand profiling database for drug repurposing and adverse side effect prediction, new fragment-based design tools for both in-situ lead optimization and scaffold-hopping, and the novel application of Matched Molecular Pairs (MMPs) analysis to study both activity cliffs and activity effects in screening results.

 Watch Now

What's New in Discovery Studio 3.5

Adrian Stevens, Senior Product Marketing Manager, BIOVIA

The latest release of Discovery Studio, 3.5, is the most comprehensive modelling and simulation solution for both small molecules and macromolecules research.

This webinar will provide an overview of the new scientific functionality available in the latest release, including new market-leading tools to calculate Antibodies Developability Index, new pH-dependent mutation energy algorithm for protein-protein binding, updated techniques for modelling antibody loops and annotating antibody sequences.

In the small molecules domain, we will showcase a brand new and peer-review validated ligand profiling database for drug repurposing and adverse side effect prediction, new fragment-based design tools for both in-situ lead optimization and scaffold-hopping, and the novel application of Matched Molecular Pairs (MMPs) analysis to study both activity cliffs and activity effects in screening results.

 Watch Now

Computational Scanning Mutagenesis of Proteins and Protein Complexes

Anne Goupil, Principal Scientist, BIOVIA
Adrian Stevens, Senior Product Marketing Manager, BIOVIA

Understanding the effect of mutation to protein stability and on protein binding affinity is key to designing protein therapeutics and also to explaining the effect of naturally occurring mutations to biological events.  We present two novel CHARMm-based computational protocols to calculate the free energy changes of protein stability and binding affinity resulting from amino acid substitutions1.  In contrast to existing published methods, the temperature dependence of energy contributions is included in the physical model.  This is known to be important in understanding and improving the thermal stability of proteins.  Furthermore, the use of Generalized Born solvation model with implicit membrane2 makes the methods applicable to transmembrane proteins.  The calculations are fast and automated so that not only alanine scanning, but complete amino acid scanning can be performed on large set of residues easily.  Validation results and possible application of the method for the purposes of protein design and bioinformatics are discussed.

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What's new in Discovery Studio 3.1

Adrian Stevens - Senior Product Marketing Manager, Accelrys

The latest release of Accelrys’ Discovery Studio 3.1 builds on the new release of Pipeline Pilot 8.5, providing enhanced scalability and job parallelization capabilities to modeling and simulation studies.  This webinar will provide an overview of the new functionality available in the latest release, including new market-leading tools to predict both the sites and propensity to aggregate in therapeutically important proteins.  Furthermore, we will also showcase enhancements to our free collaboration and visualization tools, further helping scientists to efficiently and effectively share key modeling results with research colleagues.

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Recent advances in GOLD and its implementation within modeling workflows via Discovery Studio

Recent advances in the GOLD docking program include a new scoring function, ChemPLP, and ensemble docking, which allows the user to efficiently dock against multiple models of the target protein, thus taking account of protein flexibility.

We will describe both these enhancements and present validation data showing how their use might benefit your bioactive discovery program.  We will also demonstrate how the Discovery Studio interface can be used to quickly and easily set up ensemble docking GOLD protocols and farm the jobs off into the cloud environment.

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Integration of Cresset's FieldStere within Discovery Studio 3.0

Tim Cheeseright – Director Products, Cresset
Noj Malcolm – Lead Scientist, Accelrys
Adrian Stevens – Sr. Product Marketing Manager, BIOVIA

FieldStere from Cresset identifies novel bioisosteric analogues of ligands of interest, using field-based similarity of fragments. Through the Accelrys Partner Program, Pipeline Pilot protocols have been developed that allow set-up, execution and analysis of results from FieldStere calculations within Discovery Studio 3.0. We will show the use of this integration, and how Discovery Studio 3.0 can be used to add further value through seamless application of subsequent computational analysis on the initial result set.

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Integration of Molecular Discovery's GRID within Discovery Studio 3.0 Webinar

Simon Cross – Senior Scientist & Product Manager, Molecular Discovery Ltd.
Noj Malcolm – Lead Scientist, Accelrys
Adrian Stevens – Senior Product Marketing Manager, Accelrys

GRID from Molecular Discovery has been applied in the field of structure-based drug design for over 25 years. Applications of GRID Molecular Interaction Fields range from physicochemical property prediction, virtual screening, ADME modeling, site of metabolism prediction, in addition to optimization of potency and selectivity through structure-based design or 3D QSAR techniques.  Through the Accelrys Partner Program, prototype Pipeline Pilot protocols have been developed that allow set-up, execution and analysis of results from GRID calculations within Discovery Studio 3.0. In this webinar we will discuss how and why GRID can aid your structure-based design program: the integration with Discovery Studio enables streamlined access to this science within a familiar interface, analysis of results within Discovery Studio offers potential for further value through integration with other tools and calculations.

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The Antibody Humanization Process by CDR Grafting

Leonardo Borras, Head, Protein Engineering, ESBATech LLC

The transfer of antigen binding loops from a non-human antibody donor to a human framework must be performed so that the native loop conformations are retained for binding. Often, antigen binding affinity is greatly reduced or abolished after CDR grafting. This binding activity is only restored after reverting one or more human framework residues to donor equivalents in the humanized antibody. The identification of critical framework residues that contribute to CDR conformation represents the most difficult and unpredictable step in the antibody humanization process. Here antibody modeling procedures and sequence analysis are described to assist the selection of framework mutations in the antibody humanization process.

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Discovery Studio 3.0 /Pipeline Pilot 8.0 Integration

Hongwei Huang - Principal Scientist, Accelrys

Discovery Studio is built on Pipeline Pilot™ platform technology.  It is therefore  possible for scientists to access any computational codes  available in Discovery Studio at the Pipeline Pilot level. We will show through examples how scientists can customize or build their own protocols to automate tasks and meet precise needs.

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Automatic Creation and Validation of Pharmacophores Derived from Receptor-Ligand Complexes

Tien Luu - Lead Scientist, Accelrys
Adrian Stevens - Sr. Product Marketing Manager, Accelrys

A pharmacophore is a model which represents the key physico-chemical interactions, between a receptor target and ligand, that mediate biological activity. In DS 3.0 users can automatically create a series of pharmacophore models representing a receptor-ligand complex, and have these validated with known active and inactive compounds to determine the best pharmacophore for hit/lead identification.

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Protein Design Tools in Discovery Studio 3.0: Computational Stability Prediction and Computational Alanine Scanning

Anne Goupil - Principal Scientist, Accelrys
Adrian Stevens - Sr. Product Marketing Manager, Accelrys

One of the primary goals of protein design is to engineer optimized proteins by introducing mutations. Protein thermal stability is a key issue for chemical, biotechnology and pharmaceutical industries. We will present a new set of tools available in Discovery Studio 3.0 and  show how to calculate  mutation energies as well as  predict stabilizing mutations. Similarly, Protein-protein interactions are a key components of signal transduction. Methods for predicting  energetically important amino acids (interaction hot spots) at protein-protein interfaces are of increasing interest. We will present a new set of tools available in Discovery Studio 3.0   and show how to predict  computationally derived interaction hot spots. Computational results will be compared to experimental data on a set of selected examples.

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An Introduction to Discovery Studio 3.0

Tien Luu - Lead Scientist, Accelrys
Adrian Stevens - Sr. Product Marketing Manager, Accelrys

The release of Accelrys’ Discovery Studio 3.0 in November extends our portfolio of small molecule drug design and market leading biological simulation tools and is focused on bringing new science from Accelrys and our partners, improved performance, and key enhancements to our users. This webinar will introduce users to key enhancements within the client designed to improve usability and encourage collaboration, as well as providing an overview of the new scientific developments.

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