Since the early days of computation, it has been realised that one of the aspects in which informatics could make a major impact would be in the construction of mathematical models to predict the interaction of molecules with proteins, giving rise to the study of quantitative structure-activity relationships. Later on, when the few protein structures available could be analysed with the first graphical molecular modelling packages, the automated docking of ligands into the binding cavities of proteins offered a means to generate hypotheses of protein-ligand interactions at the atomic level. These were exciting times for some of the chemists and biologists that envisaged the wealth of opportunities that integrating informatics into those traditional disciplines could offer for gaining a deeper understanding, but also widening the scope, of how small molecules interact with macromolecules.
In recent years, we have witnessed a tremendous rise in the amount of protein-ligand interaction data being generated experimentally but also an increased ability to complement them with ever more confident computational predictions. In addition, we have learned that small molecules tend to have biologically relevant affinities for multiple proteins and thus selective binding of molecules to one single protein seems to be the exception rather than the rule. And finally, our view of the interaction between molecules and proteins has been further expanded to include biological pathways, functions, side effects, organs, and diseases, to name a few, as part of the evolving global perception of a biological system. Altogether this means that the level of complexity for analysing protein-ligand interactions in the twenty-first century has increased dramatically and that innovative and integrative approaches are required.
It is in this respect that the term Molecular Informatics captures these current trends towards bringing closer together the fields of chemoinformatics and bioinformatics into an emerging new integrative field that connects small molecules and macromolecules in the context of complex chemical and biological systems. As such, it covers all aspects related to chemoinformatics (including small molecule databases, chemical information, and property calculations), to bioinformatics (including macromolecular similarity and relationships, comparative modelling, and macromolecular complexes such as protein-protein interactions), and to the interface between and beyond them (including, e.g., protein-ligand and protein-protein docking, biomolecular design, and network pharmacology). The Molecular Informatics journal provides the appropriate forum for this complex new integrative field.
Among the highlights in 2011 were Special Issues on the 18th European Symposium on Quantitative Structure-Activity Relationships (EuroQSAR 2010; guest-edited by A. Tsantili-Kakoulidou, D. K. Agrafiotis, and T. I. Oprea), and “Charting Chemical Space: Challenges and Opportunities for Artificial Intelligence and Machine Learning” (guest-edited by P. Baldi, K.-R. Müller, and G. Schneider).
In 2011, Thomson Reuters included the journal in the subject categories of “Chemistry, Medicinal” and “Mathematical & Computational Biology” and publicised the first Immediacy Index (0.593) that confirmed that Molecular Informatics has already become an active, well-recognised and indispensible journal in this field after not even two years of existence
We thank all authors and reviewers alike for their valuable contributions, and look forward to receiving your latest studies and novel developments for timely publication in Molecular Informatics.