MOE Introduction To Universitas Surabaya 20201106

Dr.
Jeremi Ongko and

Prof. Tjie Kok S.Si., M.Si., Apt., Ph.D.,
Universitas Surabaya
Introduction to MOE
November 6, 2020
Ryoichi Kataoka, Takashi Ikegami,
and Shinji Amari, MOLSIS Inc.
Molecular Operating Environment
Integrated Computer-Aided Molecular Design Platform
Small Molecules - Peptides - Biologics
1
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
2
Rich Functionalities
3
3D Molecular Visualization
• Easy-to-Use Graphical Interface

• Visualize Non-bonded Interactions
• Publication-Quality Images
• Animation and Movies
• GPU Accelerated 3D Stereo Graphics
• Mixed Virtual Reality and 3D Printing
4
Protein, Antibody and Biologics
• Protein, DNA/RNA modeling

• Antibody and biologics Design
• Epitope mapping
• Mutant analysis
• Structural biology and bioinformatics
• Protein-Protein Docking
5
Structure Based Design
• Docking simulation
• Virtual Screening
• Fragment based design
• Active site detection and analysis
• Molecular Surfaces and Electron Density
• Visualize Non-bonded Interactions
6
Small Molecules
• MOEsaic for SAR Exploration

• Pharmacophore Analysis
• Generate QSAR Models – MOE Descriptors
• Conformation Generation and Clustering
• Align and Superpose Small Molecules
• Torsion Profiles for Conformation Analysis
• Combinatorial Library Enumeration
7
Interfaces for various users
MOE/GUI
MOE/web
MOE/batch
MOE extensions for KNIME
PSILO
8
MOE/GUI
Medicinal Chemist Biologist
Computational Chemist Crystallographer

9
MOE/web
• Provide web services through the standard
infrastructure
– Web application
– SOAP API
– Database update
– Small footprint install
10
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
11
MOEsaic
• SAR explore for medicinal chemists

• Interactive matched molecular pair (MMP)
analysis
• R-group analysis
• MMP profiling / R-group profiling
• Visual analytics with property Plots and Filters.
• Virtual structure design
12
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
13
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
14
KNIME workflow example
Pharmacophore searching and docking scoring
✓ Apply the same protocol to the

various targets.
✓ Easy to edit the protocols
✓ No programming language
Copyright © 2020 MOLSIS Inc. 15

PSILO – Protein Silo
• RCSB Compliant Repository

• Depositing and Sharing the In-house Data
• Browser Interface – 3D Visualization
• Automated Project Database Curation
• 3D Interaction Search and Statistics
• Pocket Similarity Search
• Protein Structure Alignment
• Standard IT Infrastructure
• API
16
Customizable application
environment
17
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
18
Interfaces with Third Party Software
CSD - Mogul - Gold Omega - ROCS - OEB Files Quantum Mechanics

Amber Molecular Dynamics - TI
Pipeline Workflows FlexX Docking Molecular Dynamics Quantum Mechanics
SCM Quantum Mechanics

Corina DivCon
DirectFF / TEAM Forcefield
Sketcher Marvin Sketch ChemDraw Sketcher Quantum Mechanics

19
20+ years of trust
20
Citations
Paper citations:
Patent citations:
21
Citation Key Word
22
Localized technical support
23
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
24
Application
Docking of Phytochemicals to
Macrophage Inhibitory Factor
25
Preparation of Molecular System
• Receptor
– Read crystal
structure form
PDB: 1LJT
– Structure
preparation by
Protonate 3D
– Define binding
site by Site
Finder
26
Preparation of Molecular System
• Ligand
– Collect ligands
from PDB,
ChEMBL,
PubChem, etc.,
or build them by
Builder
– Store them in MDB
– Enumerate:
Protomer /
Tautomer
27
Docking (Compute | Dock)
28
Docking Result – Poses & Scores in MDB
29
Docking Result – PLIF Analyze: Bar Codes
30
Docking Result – PLIF Analyze: Ligands
31
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)
32

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Dr.

Jeremi Ongko and

Small Molecules - Peptides - Biologics

• Easy-to-Use Graphical Interface

• Protein, DNA/RNA modeling

• MOEsaic for SAR Exploration

Medicinal Chemist Biologist

Computational Chemist Crystallographer

• SAR explore for medicinal chemists

✓ Apply the same protocol to the

Copyright © 2020 MOLSIS Inc. 15

• RCSB Compliant Repository

CSD - Mogul - Gold Omega - ROCS - OEB Files Quantum Mechanics

Pipeline Workflows FlexX Docking Molecular Dynamics Quantum Mechanics

SCM Quantum Mechanics

Sketcher Marvin Sketch ChemDraw Sketcher Quantum Mechanics

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