BioSolveIT

Interactive, Visual Ligand Design with SeeSAR — A free, hands-on workshop by BioSolveIT

BioSolveIT cordially invites you to a workshop for novices in ligand design. In this "click-along" workshop, you will not only learn about interactive, visually informed ligand design, but you’ll conduct all this yourselves: Assess a protein-ligand complex with respect to “trustability” and generate Medicinal Chemistry SAR hypotheses. Dock and score molecules easily and develop your critical view on what is computed. If time permits, we will embark into the field of fragment-based ligand design (FBLD), using linking/merging, growing, and superfast rescaffolding strategies.

As the icing on the cake, we shall briefly touch the idea of navigating extremely big Chemical Spaces (trillions and beyond) — on a laptop.

All this shall be accomplished in a very playful manner using BioSolveIT's flagship design suites SeeSAR and infiniSee.

Chemical Computing Group

Computer-Aided Molecular Design

CCG is a leading developer and provider of Molecular Modeling, Simulations and Machine Learning software to Pharmaceutical and Biotechnology companies as well as Academic institutions throughout the world. CCG continuously develops new technologies with its team of mathematicians, scientists and software engineers and through scientific collaborations with customers.

Workshop 1: Structure-Based Drug Design and Ligand Modification

The course covers MOE applications for interactive structure-based drug 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. Keywords: molecular surfaces and maps; protein-ligand interactions; protein contact analysis; ligand optimization; docking

Workshop 2: Small Molecule Virtual Screening using MOE

The topics that will be covered are: Virtual screening compound libraries – descriptors, fingerprints and QSPR modeling – pharmacophore modeling – template-based docking – compound design.

Inte:Ligand

LigandScout: Advanced Workflows for Molecular Design and Discovery

LigandScout is the most user-friendly, advanced design platform available for 3D-pharmacophore modeling and virtual screening. It seamlessly integrates our advanced pharmacophore and virtual screening (VS) technologies with molecular docking, dynamics, apo site and activity profiling tools to create an inspiring and productive experience. By providing excellent prediction quality with unprecedented speed, LigandScout successfully addresses challenges in early stage drug discovery.

Workshop 1: Structure- and ligand-based modeling of kinase targets for cancer using LigandScout

Workshop 2: Molecular dynamics simulations analysis and targeting protein-protein interfaces for cancer using LigandScout

KNIME Analytics Platform

Workshop presented by Daniela Digles - Certified KNIME Trainer

The KNIME Analytics Platform is an open source workflow tool that can be used to automatize data analysis tasks. It provides a visual interface which allows the intuitive generation of workflows without programming.

Workshop 1: KNIME basics

Target audience: participants are either new to KNIME or have previous knowledge but are hesitant to change to the modern user interface. The workshop will give a general introduction to the KNIME Analytics Platform and will show how to read, modify, analyze, and visualize data.

Workshop 2: KNIME for drug discovery

Target audience: participants are already familiar with KNIME (e.g., by attending the KNIME basics workshop), but want to learn more about nodes and workflows relevant to drug discovery.

OpenEye

Improving lives through computational molecular design

Details will follow soon...

Schrödinger

Workshop 1: A beginners’ guide to system preparation, docking and designing ligands

If you are interested in learning to navigate the Schrödinger suite and how to perform docking of small molecules, join us for a hands-on workshop designed for beginners. The main Maestro interface houses all the tools that are required to bring in your starting small molecules and protein system, so that they may be prepared correctly. Once you are comfortable with the fundamentals of preparing your raw materials, we will move on to understanding more about the binding site and its features, which will help us think about how a ligand might interact with it. This forms a fundamental basis for understanding our docking results, so we will start by setting up and running docking jobs and analyzing how the resulting docked compounds fulfill the basic criteria of shape and molecular interactions that lead to the final scoring term. Finally, we will explore ligand design in a more automated fashion using the Ligand Designer GUI which facilitates on-the-fly ideation through ‘build and dock’ workflows. Using embedded libraries of building-blocks, users can modify their initial idea in many intuitive ways: from attachment points on the bound ligand; the free and viable space in the binding site; through picking specific residues in the protein or specific waters in the binding cavity to guide the design process.

Workshop 2: Efficient virtual screening: Combining ligand-based screening with QuickShape and advanced water-based scoring with WaterMap and GlideWS

In this workshop, we will assemble a modern virtual screening pipeline from start to finish. We will curate a tailored screening library by simultaneously querying catalogs of many vendors. Using QuickShape screening, we will efficiently prioritize compounds for molecular docking, reducing computational cost and focusing on promising candidates. Then, we will perform compound selection leveraging chemical properties, pharmacophore features, and diversity analysis with the Hit Analyzer tool in Maestro to identify a diverse set of potential hits. Using GlideWS, we will rescore these compounds and use the advanced visualizer in Maestro to eliminate likely false positives by analyzing protein desolvation, improving the accuracy of your screening results. Finally, we will nominate a selection of top-ranking compounds for sophisticated AB-FEP+ rescoring