WEBINAR: In
Silico Fragment-Based Drug Design: Approaches and Applications
DATE: Wednesday,
October 21 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London Time
TAGS: Scaffold Replacement / Fragment Linking / R-Group Screening
/ Medicinal Chemistry Transformations / Fragment Libraries /
Pharmacophore Models
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lNgAAI
DESCRIPTION: Fragment-based drug design (FBDD) is a key
approach in the discovery of high-quality drug candidates. As a
complement to biophysical FBDD methods, in silico FBDD uses
structure-based approaches to rapidly design and screen large libraries
of virtual compounds, allowing for the exploration of a much larger
chemical space. The webinar describes in silico FBDD methods ranging from
scaffold-hopping to fragment linking and growing in the receptor active
site. A method for generating a series of closely related derivatives
through rule-based medicinal chemistry transformations is presented. The
use of pharmacophore models and 2D/3D descriptors to guide in silico FBDD
processes is also discussed.
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VIRTUAL
WORKSHOP: Applications of Pharmacophores in Drug Design
DATE: Thursday,
October 22 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London Time
TAGS: Pharmacophore Modeling / Pharmacophore Consensus / Flexible
Alignments / Pharmacophore Searching / Protein-Ligand Interaction
Fingerprints (PLIF)
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lKwAAI
DESCRIPTION: The course describes the application of
pharmacophores in drug discovery projects and encompasses a range of
topics from pharmacophore query generation to pharmacophore refinement
and searching of structural databases. A new approach based on Extended
Hückel Theory (EHT) for producing pharmacophore models with encoded
interaction energies in the context of ligand-based and structure-based
projects will be described. The generation and analysis of protein-ligand
interaction fingerprints (PLIF) will be presented along with the
application of PLIF for producing pharmacophore queries.
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VIRTUAL
WORKSHOP: Structure-Based Drug Design and Ligand Modification
DATE: Tuesday,
October 27 2020
TIME: On Demand
TAGS: Molecular Surfaces and Maps / Ligand Interactions / Docking
/ Ligand Optimization / Ligand Selectivity / Protein Alignments and
Superposition
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lL1AAI
DESCRIPTION: The course covers MOE applications for
interactive structure based design. Examples include active site
visualization, protein-ligand contact analysis and ligand
modification/optimization in the receptor pocket. Use of the docking
module and its application to assess ligand flexibility will be
discussed. A protocol for aligning and superposing protein complexes in
the context of protein selectivity will be studied.
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WEBINAR: Creating
and Analyzing Focused Mutant Libraries for Protein Engineering
DATE: Wednesday,
October 28 2020
TIME: 11:00-11:45 Boston Time / 15:00-15:45 London Time
TAGS: Inputting Multiple Sequence Data / Mutation Frequencies /
Targeted Mutant Libraries / Protein Engineering
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lL6AAI
DESCRIPTION: Computational techniques for optimizing the
affinity of a potential therapeutic protein or antibody are described.
Experimental results from phage display may be read into MOE and analyzed
to identify promising mutation sites and specific mutations, which can
then be explored further individually and in correlation to yield
potential new leads with enhanced efficacy. Workflows for these
procedures will be described and demonstrated.
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WEBINAR: Revealing
Conformational Behavior in Solution through NMR Data Analysis
DATE: Thursday,
October 29 2020
TIME: 11:00-11:30 Boston Time / 15:00-15:30 London Time
TAGS: Conformer Generation / LowModeMD / QM Refinement / Solution
Conformer Distribution
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lLBAAY
DESCRIPTION: A dynamic, small molecule ligand may adopt a
range of conformations in solution compared to its constrained
conformation when bound to a receptor. Understanding solution behavior
may therefore provide insight into the kinetics and energetics of
binding, and thereby give clues as to how to modify the ligand to enhance
binding. This webinar illustrates the use of proton NMR NOE data to
define the solution behavior of a macrocyclic compound, through the
generation of conformers using LowModeMD, their refinement using QM
calculations, and their weighting against experimental data.
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VIRTUAL
WORKSHOP: Mining of Biomolecular Data Through an Intuitive
Web-Based Platform
DATE: Wednesday,
November 4 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London Time
TAGS: PSILO / Macromolecular repository / 3D query searching
/ Pocket similarity / Display electron density / Central repository /
Specialized protein databases
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lLGAAY
DESCRIPTION: PSILO®
is a web-based platform for the deposition and analysis of macromolecular
structural information. The workshop will describe the application of
PSILO® for mining biomolecular data. Approaches to query generation and
search result navigation in PSILO will be covered in detail; for example,
3D contact searching, and protein pocket similarity searching. The PSILO
and MOE platforms are tightly integrated, and the ability to perform
PSILO search queries directly from within MOE will also be described.
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WEBINAR: Reverse
Fingerprints (I): Application to Structural Motif Detection and Atomic
Activity Contributions
DATE: Thursday,
November 5 2020
TIME: 11:00-11:30 Boston Time / 16:00-16:30 London Time
TAGS: Molecular Fingerprints / Structural Motif Detection /
Pharmacophores / Toxicology / Fingerprint Bit Score Visualization
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lNvAAI
DESCRIPTION: Reverse fingerprints can be used to map on to
molecular structures the motifs which are important for a molecular
property of interest. This webinar covers the theory of reverse
fingerprinting and presents examples of its application to identify
pharmacophore and toxicophore motifs in different molecular series, and
to score individual atoms based on their contributions to a property.
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WEBINAR: Reverse
Fingerprints (II): Fingerprints to Pharmacophore Queries
DATE: Wednesday,
November 11 2020
TIME: 11:00-11:30 Boston Time / 16:00-16:30 London Time
TAGS: Molecular Fingerprints / Consensus Models / Pharmacophore
Elucidation / 3D Query Generation
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lO0AAI
DESCRIPTION: Different reverse fingerprints can be combined
to produce a more robust identification of important molecular motifs.
This webinar covers the basics of combining fingerprints using consensus
model theory, and demonstrates it application to motif detection and
pharmacophore query generation.
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WEBINAR: Mining
Activity Data to Guide a Medicinal Chemistry Campaign
DATE: Thursday,
November 12 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London Time
TAGS: MOEsaic / Activity Data Mining / SAR / Matched Molecular
Pairs / R-group Analysis / R-group Profiling / Free-Wilson Analysis /
Compound Suggestions
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lNlAAI
DESCRIPTION: Matched Molecular Pair analysis on an activity
data set enables finding activity cliffs and bioisosteres, providing
insight on parts of a molecule that must remain fixed or which can be
varied to advance a campaign. If activity against multiple related
targets is present, selectivity information can also be gleaned.
Analyzing and profiling the functional groups present in a data set can
point up useful routes to improving properties such as those relevant for
DMPK. This webinar will demonstrate MOEsaic, which enables these analyses
in a browser interface which is easy to use and interpret, and which
takes analysis one step further by suggesting potential new compounds,
not present in the original data sets, which are most likely to display
desirable activity and property profiles.
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WEBINAR: Protein-Protein
Docking and Epitope Analysis
DATE: Tuesday,
November 17 2020
TIME: On Demand
TAGS: Protein-Protein Docking / Molecular Surfaces / Protein
Patches / Interaction Fingerprints / Clustering / Epitope Analysis
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lNMAAY
DESCRIPTION: The MOE Protein docking application is used to
map epitopes and other protein-protein interfaces (PPI). This
automatically calculates a PPI fingerprint for each pose. The poses are
clustered using the fingerprint, and epitope residues are identified from
the top ranking clusters. The poses can then be annotated in the MOE
Window, for browsing through all the top epitopes.
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VIRTUAL
WORKSHOP: Protein Engineering and Affinity Modeling
DATE: Wednesday,
November 18 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London Time
TAGS: Protein Engineering / Protein Properties / Developability /
Hot Spot Analysis
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lLLAAY
DESCRIPTION: The workshop covers approaches for
structure-based antibody design and includes protein-protein interactions
analysis, in silico protein engineering, affinity modeling and antibody
homology modeling. The interaction of a co-crystallized antibody-antigen
complex will be studied by generating and examining the molecular
surfaces and visualizing protein-protein interactions in 3D and 2D.
Antibody properties will be evaluated using specialized calculated
protein property descriptors and analyzing protein patches.
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VIRTUAL WORKSHOP: Antibody
Modeling and Developability
DATE: Thursday,
November 19 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London
TAGS: Protein Annotation / Protein Patches / Virtual Mutagenesis /
Antibody Homology Modeling / Protein Properties / Developability
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lLQAAY
DESCRIPTION: The workshop covers the application of
computational tools for modeling the structures of antibodies, for
humanization, and for optimization of properties to enhance
developability. Examples will include the identification of glycosylation
sites and analysis of correlated pairs using a specialized antibody
database. The calculation of protein properties and their optimization to
facilitate developability as a product will also be covered.
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VIRTUAL
WORKSHOP: Applications of Pharmacophores in Drug Design
DATE: Monday,
November 23 2020
TIME: On Demand
TAGS: Pharmacophore Modeling / Pharmacophore Consensus / Flexible
Alignments / Pharmacophore Searching / Protein-Ligand Interaction
Fingerprints (PLIF)
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lNRAAY
DESCRIPTION: The course describes the application of
pharmacophores in drug discovery projects and encompasses a range of
topics from pharmacophore query generation to pharmacophore refinement
and searching of structural databases. A new approach based on Extended
Hückel Theory (EHT) for producing pharmacophore models with encoded
interaction energies in the context of ligand-based and structure-based
projects will be described. The generation and analysis of protein-ligand
interaction fingerprints (PLIF) will be presented along with the
application of PLIF for producing pharmacophore queries.
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VIRTUAL WORKSHOP:
Biologics: Protein Alignments, Modeling and Docking
DATE: Tuesday,
November 24 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London
TAGS: Protein Alignments and Superposition / Loop and Linker
Modeling / Homology Modeling / Protein- Protein Docking
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lLVAAY
DESCRIPTION: The
course covers methods for aligning protein sequences, superposing
structures, homology modeling fusion proteins and conducting
protein-protein docking. In particular, an approach for aligning and
superposing multiple structures will be described for determining
structural and surface protein variations in relation to protein property
modulation. A method for grafting and refining antibody CDR loops as well
as using a knowledge-based approach to scFv fusion protein modeling using
the MOE linker application will be described. An approach to generate
homology models of a murine antigen structure from a human template as
well as protein-protein docking of an antibody to an antigen will be discussed.
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VIRTUAL
WORKSHOP: Application of Docking and Fragment Replacement to
Structure-Based Drug Design
DATE: Wednesday,
November 25 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London
TAGS: Docking / Pharmacophore Modeling / Fragment-Based Design /
Scaffold Replacement / Protein-Ligand Interaction Fingerprints (PLIF)
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lLaAAI
DESCRIPTION: This workshop will cover some advanced workflows
for structure-based design in drug discovery projects. The application of
pharmacophores in the context of protein-ligand docking and scaffold
replacement will be included, as will the generation and analysis of
protein-ligand interaction fingerprints (PLIF). Participants will
therefore experience a broad range of computational tools that can be
brought to bear for lead generation and optimization.
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WEBINAR: Creating
and Analyzing Focused Mutant Libraries for Protein Engineering
DATE: Tuesday,
December 8 2020
TIME: On Demand
TAGS: Inputting Multiple Sequence Data / Mutation Frequencies /
Targeted Mutant Libraries / Protein Engineering
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lNWAAY
DESCRIPTION: Computational techniques for optimizing the
affinity of a potential therapeutic protein or antibody are described.
Experimental results from phage display may be read into MOE and analyzed
to identify promising mutation sites and specific mutations, which can
then be explored further individually and in correlation to yield
potential new leads with enhanced efficacy. Workflows for these
procedures will be described and demonstrated.
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WEBINAR: From
Structure to Dynamics Simulation: Workflow for Preparing, Running and
Visualizing MD Trajectories
DATE: Wednesday,
December 9 2020
TIME: 11:00-11:30 Boston Time / 16:00-16:30 London
TAGS: Structure Preparation / Force Field / Solvation / AMBER /
NAMD / Visualization / Player
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lLfAAI
DESCRIPTION: Setting up a Molecular Dynamics simulation
starting from a protein PDB structure can be challenging. It involves:
data preparation, force field parameterization, running protocols and
trajectory analysis/visualization. MOE provides a streamlined interface
which allows for easy setup, execution and visualization of MD
trajectories via AMBER, NAMD or the internal MD engine. In this webinar,
the complete workflow to run MD simulations will be introduced.
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WEBINAR: Advanced
Small Molecule Docking
DATE: Thursday,
December 10 2020
TIME: 11:00-11:45 Boston Time / 16:00-16:45 London
TAGS: Structure Preparation / Protein Binding Site Visualization /
Template-Based Docking / Covalent Docking / Pharmacophores / Protein-Ligand
Interaction Fingerprints (PLIF) / Multiple Processor Calculations
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lLkAAI
DESCRIPTION: Advanced docking workflows encountered in drug
discovery projects will be described, which include a range of related
topics from the application of pharmacophore constraints in docking to
the analysis of protein-ligand interaction fingerprints (PLIF) generated
from docked poses. Examples include: (1) general docking with applied
pharmacophore constraints, (2) template-based docking using a scaffold or
fragment to guide placement, and (3) covalent docking to generate, rank
and score ligands that are covalently bound to a protein/receptor.
Leveraging multiple processing capacity will also be presented.
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WEBINAR: In
Silico Fragment-Based Drug Design: Approaches and Applications
DATE: Wednesday,
December 16 2020
TIME: On Demand
TAGS: Scaffold Replacement / Fragment Linking / R-Group Screening
/ Medicinal Chemistry Transformations / Fragment Libraries /
Pharmacophore Models
REGISTER: https://www.chemcomp.com/Events.htm?r=7010z0000017lNbAAI
DESCRIPTION: Fragment-based drug design (FBDD) is a key
approach in the discovery of high-quality drug candidates. As a
complement to biophysical FBDD methods, in silico FBDD uses
structure-based approaches to rapidly design and screen large libraries
of virtual compounds, allowing for the exploration of a much larger
chemical space. The webinar describes in silico FBDD methods ranging from
scaffold-hopping to fragment linking and growing in the receptor active
site. A method for generating a series of closely related derivatives
through rule-based medicinal chemistry transformations is presented. The
use of pharmacophore models and 2D/3D descriptors to guide in silico FBDD
processes is also discussed.
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