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MOE Introduction To Universitas Surabaya 20201106
MOE Introduction To Universitas Surabaya 20201106
Introduction to MOE
November 6, 2020
Ryoichi Kataoka, Takashi Ikegami,
and Shinji Amari, MOLSIS Inc.
Molecular Operating Environment
Integrated Computer-Aided Molecular Design Platform
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Copyright © 2020 MOLSIS Inc.
Contents
• Features of MOE
– Rich functionalities
– Interfaces fitted for various users
• MOE/GUI
• MOE/web
• MOE/batch
• MOE extensions for KNIME
• PSILO
– Customizable application environment
– 20+ years of trust
• Localized technical support
• Application
– Docking of phytochemicals to macrophage inhibitory factor
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Copyright © 2020 MOLSIS Inc.
Rich Functionalities
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3D Molecular Visualization
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Protein, Antibody and Biologics
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Structure Based Design
• Docking simulation
• Virtual Screening
• Fragment based design
• Active site detection and analysis
• Molecular Surfaces and Electron Density
• Visualize Non-bonded Interactions
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Small Molecules
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Interfaces for various users
MOE/GUI
MOE/web
MOE/batch
MOE extensions for KNIME
PSILO
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Copyright © 2020 MOLSIS Inc.
MOE/GUI
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Copyright © 2020 MOLSIS Inc.
MOE/web functionalities
• Web application
– MOEsaic - SAR Explorer
– Antibody Modeling
– Small Molecule properties, etc..
• SOAP API
– Pharmacophore search
– Project database search
– Mogul analysis
– QM calculation
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Copyright © 2020 MOLSIS Inc.
MOEsaic
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Copyright © 2020 MOLSIS Inc.
MOE/batch
• Running MOE on the console mode
– Faster calculation than graphics mode
– Efficiently use tokens
• MOE/smp
– Distributed computing by multiple CPU cores
– Cloud computing
– Processing large amounts of data
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Copyright © 2020 MOLSIS Inc.
MOE extensions for KNIME
• KNIME (https://www.knime.com/)
– Open source platform that automates linkage,
integration, and analysis of all data
– The user defines the data processing flow by
connecting the node icons that define single
processing.
• 150+ MOE nodes
– Database processing
– Compound processing
– Molecular simulation
– Data plotting
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Copyright © 2020 MOLSIS Inc.
KNIME workflow example
Pharmacophore searching and docking scoring
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Copyright © 2020 MOLSIS Inc.
Customizable application
environment
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Copyright © 2020 MOLSIS Inc.
Development Environment on MOE
• SVL – Scientific Vector Language
– Programming language for MOE application development
– User can refer to the source codes of MOE application
– Allow users to customize or develop a new application
• Provide original program from MOLSIS
– ASEDock: Docking simulation
– AutoGPA: 3D-QSAR
– AutoQSAR: Build a QSAR model automatically
– QSAR Evolution: Build a QSAR with genetic algorithm
– HLA Modeler: Homology modeling for HLA
– HLABAP: HLA-Binding Peptide Predictor
– MOE-QFSS: Quick Federated Structure Search
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Copyright © 2020 MOLSIS Inc.
Interfaces with Third Party Software
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Citations
Paper citations:
Patent citations:
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Citation Key Word
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Localized technical support
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Copyright © 2020 MOLSIS Inc.
Technical Support
• In MOLSIS, we have 30+ years experience of
molecular modeling and simulations.
– Training course
– Technical support by e-mail, telephone and web
meeting.
– Provide the customized program.
– Local technical support available for Customers in
China and Korea
• CCG provides ‘SVL Exchange’ site
– Add on applications for MOE
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Copyright © 2020 MOLSIS Inc.
Application
Docking of Phytochemicals to
Macrophage Inhibitory Factor
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Copyright © 2020 MOLSIS Inc.
Preparation of Molecular System
• Receptor
– Read crystal
structure form
PDB: 1LJT
– Structure
preparation by
Protonate 3D
– Define binding
site by Site
Finder
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Copyright © 2020 MOLSIS Inc.
Preparation of Molecular System
• Ligand
– Collect ligands
from PDB,
ChEMBL,
PubChem, etc.,
or build them by
Builder
– Store them in MDB
– Enumerate:
Protomer /
Tautomer
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Docking (Compute | Dock)
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Docking Result – Poses & Scores in MDB
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Docking Result – PLIF Analyze: Bar Codes
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Docking Result – PLIF Analyze: Ligands
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Copyright © 2020 MOLSIS Inc.
Contacts
Sole Distributor
Japan & Asia:
MOLSIS INC.
Gyeonggi E-mail: sales@molsis.co.jp (Sales and Contract)
Local partner E-mail: support@molsis.co.jp (Technical Support)
Korea:
BITEK CHEMS INC.
E-mail: info@bitekchems.com
Tokyo
Local partner
China:
Shanghai 康昱盛信息科技有限公司
E-mail: marketing@cloudscientific.com (Marketing)
E-mail: sales@cloudscientific.com (Sales)
E-mail: support@cloudscientific.com (Support)
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Copyright © 2020 MOLSIS Inc.