Free learning resources

• Tutorial

Potency Predictions for RNA-Binding Small Molecules Using RB-FEP

Performing RB-FEP calculations to predict binding affinities for congeneric ligands binding to an RNA receptor.

• Tutorial

Forming RNA – Ligand Interactions with Ligand Designer

Modify ligand bound to RNA receptor to improve binding affinity using Ligand Designer.

• Tutorial

Small Molecule – Oligonucleotide Docking with Glide

Generate receptor grid, dock co-crystal and congeneric ligands, and analyze the results.

• Tutorial

Analyzing Binding Sites of Nucleic Acids with SiteMap

Identification and evaluation of binding sites in nucleic acid structures with SiteMap.

• Tutorial

Preparing Nucleic Acid Structures

Visualization and analysis of interactions in nucleic acid structures.

• Tutorial

Preparing Nucleic Acid Structures

Preparation of nucleic acid structures for modeling applications.

• Documentation

WaterMap

Efficiently converged MD simulations are run with explicit water molecules, and resultant trajectories are analyzed to cluster hydration sites.

• Documentation

SiteMap

Identify binding sites, including allosteric binding sites and protein-protein interfaces, and evaluate their druggability.

• Documentation

Shape Screening

A ligand-based workflow for efficiently screening ultra-large purchasable or synthesizable compound libraries.

• Documentation

QSite

A multi-scale simulation tool that utilizes the QM/MM method, which combines the principles of quantum mechanics and molecular mechanics.

• Documentation

QikProp

An advanced tool for predicting pharmacokinetic and physicochemical (ADME) properties of small organic molecules based on the full 3D molecular structure.

PyMOL

High quality visual representations of molecular structures for visualizing, analyzing, exploring and understanding three dimensional structures of proteins, nucleic acids and other molecules, allowing researchers to analyze and interpret complex biological data.