IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein–Ligand Interactions

• Published in: ChemMedChem 2018-03, Vol.13 (6), p.507-510
• Main Authors: Da Silva, Franck, Desaphy, Jeremy, Rognan, Didier
• Format: Article
• Language: English
• Subjects: cavity; Communication; Communications; drug design; fingerprints; Graphical representations; interactions; Knowledge acquisition; Ligands; Models, Molecular; Molecular interactions; Protein structure; Proteins - chemistry; Software; Topology; Typing; virtual screening; Water chemistry
• ISSN: 1860-7179; 1860-7187
• DOI: 10.1002/cmdc.201700505

Structure‐based ligand design requires an exact description of the topology of molecular entities under scrutiny. IChem is a software package that reflects the many contributions of our research group in this area over the last decade. It facilitates and automates many tasks (e.g., ligand/cofactor atom typing, identification of key water molecules) usually left to the modeler's choice. It therefore permits the detection of molecular interactions between two molecules in a very precise and flexible manner. Moreover, IChem enables the conversion of intricate three‐dimensional (3D) molecular objects into simple representations (fingerprints, graphs) that facilitate knowledge acquisition at very high throughput. The toolkit is an ideal companion for setting up and performing many structure‐based design computations. Taming complexity: IChem is a suite of software dedicated to the analysis and comparison of three‐dimensional molecular objects. It converts an intricate three‐dimensional information into much simpler fingerprints or graphs, thereby enabling high‐throughput comparisons and fueling machine learning models for predicting important features like protein–protein interfaces, druggable cavities, interaction patterns, and binding poses.