Molecular Modeling Computational Chemistry Medicinal Chemistry Enzyme Design Software Development

for the study and design of chemobiological systems

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The Mission

Our mission is to develop and apply molecular modeling tools for the study and design of pharmacological and biotechnological systems.

The focus

We work on the modeling of a variety of fields mainly centered on the development of chemobiological hybdrids like de novo enzymes or drug design projects. In this aspect we work primarily on antipathogenic targets and recently orient our studies towards natural products and contaminants.

The Strategy

In our research, we use a broad range of methods and eventually combine them in multi-level platform. We also work intensively on developing our own tools including new docking approaches and molecular builders. Our expertise range from Homology Modeling, Molecular Dynamics, QM/MM, protein-ligand docking approaches. We also actively participate in the development of new tools to deal with metallic moieties in biological system.


Led by Prof. Jean-Didier Maréchal (cv), InSiliChem is a team that focuses on the modeling of systems at the interface between chemistry and biology. We have broad research interests although our primarily fields of research are the development of new chemobiological hybrids (e.g. artificial enzymes, metallopeptides, biomarkers,…) as well as the identification of bioactive compounds and the study of their pharmacological profiles (e.g. screening of natural compounds against therapeutic drugs, transition metal based therapies, prediction of P450 metabolism,…). One of the particularity of the group is to focus on metal mediated processes.
Our work is sustained by a large number of methods from protein-ligand docking to QM/MM but we also intensively work on structural bioinformatics and computational chemistry methodological developments like a multi-scale platform, new analysing tools and a modular molecular sketcher called GaudiMM. Most of these efforts are performed using Python as a principal scripting language.
We have a large network of collaborations worldwide both with experimental and theoretical groups leader in these fields.



Our group has a high level of research production and publication. In this section, some of the latest publications are shown.

Design and evolution of chimeric streptavidin for protein-enabled dual gold catalysis
F. Christoffel, et al.

Nat. Catal., 2022 (Q1, IF: 40.706)

Selective recognition of A/T-rich DNA 3-way junctions with a three-fold symmetric tripeptide.
J. Gómez-González, et al.

Chem. Comm., 2021 (Q1, IF: 6.22)

Impact of Cu(II) and Al(III) on the conformational landscape of Amyloidβ 1-42
L. Roldán-Martín, et al.

PCCP, 2021 (Q1, IF: 3.430)

BioMetAll: Identifying Metal-Binding Sites in Proteins fromBackbone Preorganization
J.E. Sánchez-Aparicio, et al.

JCIM, 2021 (Q1, IF: 4.549)

Molecular Modeling for Artificial Metalloenzyme Design and Optimization
L. Cotchico, et al.

Acc. Chem. Res., 2020 (Q1, IF: 21.661)

GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm
J.E. Sánchez-Aparicio, et al.

Int. J. Mol. Sci, 2019 (Q1, IF: 4.556)

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