A powerful suite of C++ tools engineered to accelerate, optimize, and empower your molecular discoveries in structure-based design scenarios.

Download IChem Quick start
6 Modules
1 Executable
0 Build steps
5.3.9 Current version

Structure-based design, end to end

IChem detects, analyses and compares the interactions a ligand makes with its target. It automates the fiddly preparation work — ligand and cofactor atom typing, identification of key water molecules — then converts intricate 3D objects into simple representations, fingerprints and graphs, that can be compared at very high throughput.

That shift is what makes the difference in practice. Once a binding mode is a bit string or a graph, questions that were visual and manual become computational: which docking pose reproduces the crystallographic interactions, which pockets across a structural database resemble this one, which fragment of a bound ligand is doing the work. Everything runs from a single executable with no build step and no dependencies beyond the standard C++ runtime.

The six modules

Each turns a 3D structure into something measurable. Follow any card through to its worked tutorial.

Realign

Align proteins, cavities or ligands.

Tutorial
IFP

Converts the 3D structure of protein (nucleic acid) – ligand complexes into a residue-based interaction fingerprint, computes pairwise similarities of interaction fingerprints.

Tutorial
INTS

Lists in a table non-covalent interactions (hydrophobic, aromatics, hydrogen bonds, ionic bonds, halogen bonds, etc.) from a 3D structure.

Tutorial
GRIM

Converts the 3D structure of protein (nucleic acid) – ligand complexes into a generic 3D graph, computes pairwise similarities of graphs.

Tutorial
VolSite

Detects cavities and estimates their druggability, computes a cavity fingerprint.

Tutorial
Utils

Various goodies: computes buried surface areas, fragments a protein-bound ligand according to RECAP rules.

Tutorial

Getting started

Download the executable and its data folder, set ICHEM_LIB, and you are running. The quick start goes from a PDB entry to an interaction fingerprint in two commands; the tutorials then work through each module with commands you can reproduce against the supplied dataset.

IChem is developed by the Structural Chemogenomics group at the Laboratoire d'Innovation Thérapeutique in Strasbourg. The papers behind each method are collected in the Literature corner.